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experiment_config.yaml
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version: "6.0"
experiment:
UMI: yes
SNP: yes
scripts:
location: path/to/scripts/perl
#UMI_script: NA -- same as SNP script
SNP_script: ast_snpv72.pl
asymagic: as2.pl
s2: step2v56.pl
output:
#### step 2 only:
result: output/test_out.txt
## the following line should be uncommented if you don't want this YAML file copied to output
#~ output_yaml: no
# if DEBUG: 1 -- diagnostic info will be printed after each gene
diagnostics:
DEBUG: 1
use_existing_sorted_SAM: 0
leave_SAM: 1
#~ SAMsubsampleFraction: 05
##[01..99] ^ for debug purposes only! for real analysis: comment it out!
## In step2.pl defines % of BAM to subsample. Useful for a speedup when testing
##
alignment:
#file_names:
### the following applies to step 1:::
fastq_dir: /path/to/fastq/
R1: R1.fastq
R2: R2.fastq
reference: mm10
### the following applies to step 1 + step 2:::
SAM_name_base: example_mm10
SAM_location: sam/example/
#### Description of targets (step2)
genes:
AdNp2:
SNP: TCCCTG[N/N]CAGCTA
position: chr18:80125935-80128475
#~ SKIP:
Adamtsl4:
SNP: GGGGAA[N/N]GACCAC
position: chr3:95675004-95677646
Dlc1:
SNP: AAGAAC[N/N]GAGCAA
position: chr8:36566539-36569311
DNajc12:
SNP: CAAAAT[N/N]TAGACT
position: chr10:63407514-63410040
Gprasp1:
SNP: ACGCTT[N/N]TTGTGT
position: chrX:135802055-135804668
SmtNl2:
SNP: ATTTCT[N/N]TGTGGG
position: chr11:72388914-72391598
3830406C13Rik:
SNP: TAAGCC[N/N]GAAGAT
position: chr14:12301702-12304431
Slc25a37:
SNP: TATGAA[N/N]AACAAA
position: chr14:69240651-69243339
Tpst1:
SNP: TTGAAG[N/N]TGGCAT
position: chr5:130134244-130136932
samples_barcodes:
aNA_NA_5_DBJ28_R1_d12: AGTCAA_GTGAAA
bKdm1a_CDS_1_DBJ28_R1_d12: AGTTCC_GTGGCC
cCbx3_CDS_1_DBJ28_R1_d12: ATGTCA_GTTTCG
dClspn_CDS_1_DBJ28_R1_d12: CCGTCC_CGTACG
eJarid2_CDS_1_DBJ28_R1_d12: GTAGAG_GAGTGG
fDnmt3a_CDS_1_DBJ28_R1_d12: GTCCGC_GGTAGC
gCul3_3UTR_1_DBJ28_R1_d12: GTGAAA_AGTCAA
hAurka_CDS_1_DBJ28_R1_d12: GTGGCC_AGTTCC
iBmpr2_CDS_1_DBJ28_R1_d12: GTTTCG_ATGTCA
jKdm1a_CDS_2_DBJ28_R1_d12: CGTACG_CCGTCC
kAsh2l_3UTR_1_DBJ28_R1_d12: GAGTGG_GTAGAG
lAsh2l_CDS_2_DBJ28_R1_d12: GGTAGC_GTCCGC
mDnmt3a_CDS_2_DBJ28_R1_d12: AGTCAA_CACGAT
nAcvr1_CDS_1_DBJ28_R1_d12: AGTTCC_CACTCA
oGins3_CDS_1_DBJ28_R1_d12: ATGTCA_CAGGCG
pCdyl_CDS_1_DBJ28_R1_d12: CCGTCC_CATGGC
qClspn_3UTR_2_DBJ28_R1_d12: GTAGAG_CATTTT
rBrca2_CDS_1_DBJ28_R1_d12: GTCCGC_CCAACA
sBmpr2_CDS_2_DBJ28_R1_d12: GTGAAA_ACTGAT
tCul3_CDS_2_DBJ28_R1_d12: GTGGCC_ATGAGC
uHdac3_3UTR_1_DBJ28_R1_d12: GTTTCG_ATTCCT
vAcvr1b_CDS_1_DBJ28_R1_d12: CGTACG_CAAAAG
wHdac3_CDS_2_DBJ28_R1_d12: GAGTGG_CAACTA
xCbx3_CDS_2_DBJ28_R1_d12: GGTAGC_CACCGG
yFbxo8_CDS_1_DBJ28_R1_d12: AGTCAA_TACAGC
zJarid2_CDS_2_DBJ28_R1_d12: AGTTCC_TATAAT
aaBmpr2_CDS_3_DBJ28_R1_d12: ATGTCA_TCATTC
abDnmt3a_CDS_3_DBJ28_R1_d12: CCGTCC_TCCCGA
acJarid2_CDS_3_DBJ28_R1_d12: GTAGAG_TCGAAG
adAurka_CDS_2_DBJ28_R1_d12: GTCCGC_TCGGCA
aeCul3_CDS_3_DBJ28_R1_d12: GTGAAA_CGGAAT
#~ SKIP:
afLUCIFERASE_CDS_4_DBJ28_R1_d12: GTGGCC_CTAGCT
agAcvr1b_CDS_2_DBJ28_R1_d12: GTTTCG_CTATAC
ahAurka_CDS_3_DBJ28_R1_d12: CGTACG_CTCAGA
aiAsh2l_CDS_3_DBJ28_R1_d12: GAGTGG_GACGAC
ajGins3_CDS_2_DBJ28_R1_d12: GGTAGC_TAATCG
akCbx3_CDS_3_DBJ28_R1_d12: ACTGAT_GTGAAA
alCdyl_CDS_2_DBJ28_R1_d12: ATGAGC_GTGGCC
amBrca2_CDS_2_DBJ28_R1_d12: ATTCCT_GTTTCG
anAff1_CDS_1_DBJ28_R1_d12: CAAAAG_CGTACG
aoAcvr1_CDS_2_DBJ28_R1_d12: CAACTA_GAGTGG
apHdac3_CDS_3_DBJ28_R1_d12: CACCGG_GGTAGC
aqAcvr1b_CDS_3_DBJ28_R1_d12: CACGAT_AGTCAA
arBmpr2_CDS_4_DBJ28_R1_d12: CACTCA_AGTTCC
asGFP_CDS_4_DBJ28_R1_d12: CAGGCG_ATGTCA
atCdyl_3UTR_3_DBJ28_R1_d12: CATGGC_CCGTCC
auAcvr1_CDS_3_DBJ28_R1_d12: CATTTT_GTAGAG
avClspn_3UTR_3_DBJ28_R1_d12: CCAACA_GTCCGC
awH2afy_CDS_1_DBJ28_R1_d12: ACTGAT_CACGAT
axJarid2_CDS_4_DBJ28_R1_d12: ATGAGC_CACTCA
ayGins3_CDS_3_DBJ28_R1_d12: ATTCCT_CAGGCG
azCbx3_3UTR_4_DBJ28_R1_d12: CAAAAG_CATGGC
baHdac3_CDS_4_DBJ28_R1_d12: CAACTA_CATTTT
bbCul3_CDS_4_DBJ28_R1_d12: CACCGG_CCAACA
bcKdm1a_CDS_3_DBJ28_R1_d12: CACGAT_ACTGAT
bdBrca2_CDS_3_DBJ28_R1_d12: CACTCA_ATGAGC
beAff1_CDS_2_DBJ28_R1_d12: CAGGCG_ATTCCT
bfClspn_CDS_4_DBJ28_R1_d12: CATGGC_CAAAAG
bgHdac3_CDS_5_DBJ28_R1_d12: CATTTT_CAACTA
bhAcvr1_CDS_4_DBJ28_R1_d12: CCAACA_CACCGG
biH2afy_CDS_2_DBJ28_R1_d12: ACTGAT_TACAGC
bjCbx3_CDS_5_DBJ28_R1_d12: ATGAGC_TATAAT
bkKdm1a_CDS_4_DBJ28_R1_d12: ATTCCT_TCATTC
blDnmt3a_CDS_4_DBJ28_R1_d12: CAAAAG_TCCCGA
bmCdyl_CDS_4_DBJ28_R1_d12: CAACTA_TCGAAG
bnAff1_CDS_3_DBJ28_R1_d12: CACCGG_TCGGCA
boH2afy_CDS_3_DBJ28_R1_d12: CACGAT_CGGAAT
bpCdyl_CDS_5_DBJ28_R1_d12: CACTCA_CTAGCT
bqJarid2_3UTR_5_DBJ28_R1_d12: CAGGCG_CTATAC
brAcvr1b_CDS_4_DBJ28_R1_d12: CATGGC_CTCAGA
bsDnmt3a_CDS_5_DBJ28_R1_d12: CATTTT_GACGAC
btAff1_3UTR_4_DBJ28_R1_d12: CCAACA_TAATCG
buGins3_CDS_4_DBJ28_R1_d12: CGGAAT_GTGAAA
bvAff1_CDS_5_DBJ28_R1_d12: CTAGCT_GTGGCC
bwH2afy_CDS_4_DBJ28_R1_d12: CTATAC_GTTTCG
bxAcvr1b_CDS_5_DBJ28_R1_d12: CTCAGA_CGTACG
byBmpr2_3UTR_5_DBJ28_R1_d12: GACGAC_GAGTGG
bzFbxo8_CDS_2_DBJ28_R1_d12: TAATCG_GGTAGC
caAsh2l_CDS_4_DBJ28_R1_d12: TACAGC_AGTCAA
cbAurka_CDS_4_DBJ28_R1_d12: TATAAT_AGTTCC
ccKdm1a_CDS_5_DBJ28_R1_d12: TCATTC_ATGTCA
cdAsh2l_CDS_5_DBJ28_R1_d12: TCCCGA_CCGTCC
ceFbxo8_CDS_3_DBJ28_R1_d12: TCGAAG_GTAGAG
cfFbxo8_3UTR_4_DBJ28_R1_d12: TCGGCA_GTCCGC
cgClspn_CDS_5_DBJ28_R1_d12: CGGAAT_CACGAT
chCul3_CDS_5_DBJ28_R1_d12: CTAGCT_CACTCA
ciFbxo8_CDS_5_DBJ28_R1_d12: CTATAC_CAGGCG
cjBrca2_3UTR_4_DBJ28_R1_d12: CTCAGA_CATGGC
ckAcvr1_CDS_5_DBJ28_R1_d12: GACGAC_CATTTT
clAurka_CDS_5_DBJ28_R1_d12: TAATCG_CCAACA
cmBrca2_CDS_5_DBJ28_R1_d12: TACAGC_ACTGAT
cnGins3_3UTR_5_DBJ28_R1_d12: TATAAT_ATGAGC
coNA_NA_6_DBJ28_R1_d12: TCATTC_ATTCCT
cpNA_NA_7_DBJ28_R1_d12: TCCCGA_CAAAAG
cqH2afy_CDS_5_DBJ28_R1_d12: TCGAAG_CAACTA
crNA_NA_8_DBJ28_R1_d12: TCGGCA_CACCGG
aNA_NA_5_DBJ28_R2_d12: AGTCAA_AGTCAA
bKdm1a_CDS_1_DBJ28_R2_d12: AGTTCC_AGTTCC
cCbx3_CDS_1_DBJ28_R2_d12: ATGTCA_ATGTCA
dClspn_CDS_1_DBJ28_R2_d12: CCGTCC_CCGTCC
eJarid2_CDS_1_DBJ28_R2_d12: GTAGAG_GTAGAG
fDnmt3a_CDS_1_DBJ28_R2_d12: GTCCGC_GTCCGC
gCul3_3UTR_1_DBJ28_R2_d12: GTGAAA_GTGAAA
hAurka_CDS_1_DBJ28_R2_d12: GTGGCC_GTGGCC
iBmpr2_CDS_1_DBJ28_R2_d12: GTTTCG_GTTTCG
jKdm1a_CDS_2_DBJ28_R2_d12: CGTACG_CGTACG
kAsh2l_3UTR_1_DBJ28_R2_d12: GAGTGG_GAGTGG
lAsh2l_CDS_2_DBJ28_R2_d12: GGTAGC_GGTAGC
mDnmt3a_CDS_2_DBJ28_R2_d12: AGTCAA_ACTGAT
nAcvr1_CDS_1_DBJ28_R2_d12: AGTTCC_ATGAGC
oGins3_CDS_1_DBJ28_R2_d12: ATGTCA_ATTCCT
pCdyl_CDS_1_DBJ28_R2_d12: CCGTCC_CAAAAG
qClspn_3UTR_2_DBJ28_R2_d12: GTAGAG_CAACTA
rBrca2_CDS_1_DBJ28_R2_d12: GTCCGC_CACCGG
sBmpr2_CDS_2_DBJ28_R2_d12: GTGAAA_CACGAT
tCul3_CDS_2_DBJ28_R2_d12: GTGGCC_CACTCA
uHdac3_3UTR_1_DBJ28_R2_d12: GTTTCG_CAGGCG
vAcvr1b_CDS_1_DBJ28_R2_d12: CGTACG_CATGGC
wHdac3_CDS_2_DBJ28_R2_d12: GAGTGG_CATTTT
xCbx3_CDS_2_DBJ28_R2_d12: GGTAGC_CCAACA
yFbxo8_CDS_1_DBJ28_R2_d12: AGTCAA_CGGAAT
zJarid2_CDS_2_DBJ28_R2_d12: AGTTCC_CTAGCT
aaBmpr2_CDS_3_DBJ28_R2_d12: ATGTCA_CTATAC
abDnmt3a_CDS_3_DBJ28_R2_d12: CCGTCC_CTCAGA
acJarid2_CDS_3_DBJ28_R2_d12: GTAGAG_GACGAC
adAurka_CDS_2_DBJ28_R2_d12: GTCCGC_TAATCG
aeCul3_CDS_3_DBJ28_R2_d12: GTGAAA_TACAGC
afLUCIFERASE_CDS_4_DBJ28_R2_d12: GTGGCC_TATAAT
agAcvr1b_CDS_2_DBJ28_R2_d12: GTTTCG_TCATTC
ahAurka_CDS_3_DBJ28_R2_d12: CGTACG_TCCCGA
aiAsh2l_CDS_3_DBJ28_R2_d12: GAGTGG_TCGAAG
ajGins3_CDS_2_DBJ28_R2_d12: GGTAGC_TCGGCA
akCbx3_CDS_3_DBJ28_R2_d12: ACTGAT_AGTCAA
alCdyl_CDS_2_DBJ28_R2_d12: ATGAGC_AGTTCC
amBrca2_CDS_2_DBJ28_R2_d12: ATTCCT_ATGTCA
anAff1_CDS_1_DBJ28_R2_d12: CAAAAG_CCGTCC
aoAcvr1_CDS_2_DBJ28_R2_d12: CAACTA_GTAGAG
apHdac3_CDS_3_DBJ28_R2_d12: CACCGG_GTCCGC
aqAcvr1b_CDS_3_DBJ28_R2_d12: CACGAT_GTGAAA
arBmpr2_CDS_4_DBJ28_R2_d12: CACTCA_GTGGCC
asGFP_CDS_4_DBJ28_R2_d12: CAGGCG_GTTTCG
atCdyl_3UTR_3_DBJ28_R2_d12: CATGGC_CGTACG
auAcvr1_CDS_3_DBJ28_R2_d12: CATTTT_GAGTGG
avClspn_3UTR_3_DBJ28_R2_d12: CCAACA_GGTAGC
awH2afy_CDS_1_DBJ28_R2_d12: ACTGAT_ACTGAT
axJarid2_CDS_4_DBJ28_R2_d12: ATGAGC_ATGAGC
ayGins3_CDS_3_DBJ28_R2_d12: ATTCCT_ATTCCT
azCbx3_3UTR_4_DBJ28_R2_d12: CAAAAG_CAAAAG
baHdac3_CDS_4_DBJ28_R2_d12: CAACTA_CAACTA
bbCul3_CDS_4_DBJ28_R2_d12: CACCGG_CACCGG
bcKdm1a_CDS_3_DBJ28_R2_d12: CACGAT_CACGAT
bdBrca2_CDS_3_DBJ28_R2_d12: CACTCA_CACTCA
beAff1_CDS_2_DBJ28_R2_d12: CAGGCG_CAGGCG
bfClspn_CDS_4_DBJ28_R2_d12: CATGGC_CATGGC
bgHdac3_CDS_5_DBJ28_R2_d12: CATTTT_CATTTT
bhAcvr1_CDS_4_DBJ28_R2_d12: CCAACA_CCAACA
biH2afy_CDS_2_DBJ28_R2_d12: ACTGAT_CGGAAT
bjCbx3_CDS_5_DBJ28_R2_d12: ATGAGC_CTAGCT
bkKdm1a_CDS_4_DBJ28_R2_d12: ATTCCT_CTATAC
blDnmt3a_CDS_4_DBJ28_R2_d12: CAAAAG_CTCAGA
bmCdyl_CDS_4_DBJ28_R2_d12: CAACTA_GACGAC
bnAff1_CDS_3_DBJ28_R2_d12: CACCGG_TAATCG
boH2afy_CDS_3_DBJ28_R2_d12: CACGAT_TACAGC
bpCdyl_CDS_5_DBJ28_R2_d12: CACTCA_TATAAT
bqJarid2_3UTR_5_DBJ28_R2_d12: CAGGCG_TCATTC
brAcvr1b_CDS_4_DBJ28_R2_d12: CATGGC_TCCCGA
bsDnmt3a_CDS_5_DBJ28_R2_d12: CATTTT_TCGAAG
btAff1_3UTR_4_DBJ28_R2_d12: CCAACA_TCGGCA
buGins3_CDS_4_DBJ28_R2_d12: CGGAAT_AGTCAA
bvAff1_CDS_5_DBJ28_R2_d12: CTAGCT_AGTTCC
bwH2afy_CDS_4_DBJ28_R2_d12: CTATAC_ATGTCA
bxAcvr1b_CDS_5_DBJ28_R2_d12: CTCAGA_CCGTCC
byBmpr2_3UTR_5_DBJ28_R2_d12: GACGAC_GTAGAG
bzFbxo8_CDS_2_DBJ28_R2_d12: TAATCG_GTCCGC
caAsh2l_CDS_4_DBJ28_R2_d12: TACAGC_GTGAAA
cbAurka_CDS_4_DBJ28_R2_d12: TATAAT_GTGGCC
ccKdm1a_CDS_5_DBJ28_R2_d12: TCATTC_GTTTCG
cdAsh2l_CDS_5_DBJ28_R2_d12: TCCCGA_CGTACG
ceFbxo8_CDS_3_DBJ28_R2_d12: TCGAAG_GAGTGG
cfFbxo8_3UTR_4_DBJ28_R2_d12: TCGGCA_GGTAGC
cgClspn_CDS_5_DBJ28_R2_d12: CGGAAT_ACTGAT
chCul3_CDS_5_DBJ28_R2_d12: CTAGCT_ATGAGC
ciFbxo8_CDS_5_DBJ28_R2_d12: CTATAC_ATTCCT
cjBrca2_3UTR_4_DBJ28_R2_d12: CTCAGA_CAAAAG
ckAcvr1_CDS_5_DBJ28_R2_d12: GACGAC_CAACTA
clAurka_CDS_5_DBJ28_R2_d12: TAATCG_CACCGG
cmBrca2_CDS_5_DBJ28_R2_d12: TACAGC_CACGAT
cnGins3_3UTR_5_DBJ28_R2_d12: TATAAT_CACTCA
coNA_NA_6_DBJ28_R2_d12: TCATTC_CAGGCG
cpNA_NA_7_DBJ28_R2_d12: TCCCGA_CATGGC
cqH2afy_CDS_5_DBJ28_R2_d12: TCGAAG_CATTTT
crNA_NA_8_DBJ28_R2_d12: TCGGCA_CCAACA
aNA_NA_5_DBJ28_R1_d19: AGTCAA_AGTTCC
bKdm1a_CDS_1_DBJ28_R1_d19: AGTTCC_ATGTCA
cCbx3_CDS_1_DBJ28_R1_d19: ATGTCA_CCGTCC
dClspn_CDS_1_DBJ28_R1_d19: CCGTCC_GTAGAG
eJarid2_CDS_1_DBJ28_R1_d19: GTAGAG_GTCCGC
fDnmt3a_CDS_1_DBJ28_R1_d19: GTCCGC_GTGAAA
gCul3_3UTR_1_DBJ28_R1_d19: GTGAAA_GTGGCC
hAurka_CDS_1_DBJ28_R1_d19: GTGGCC_GTTTCG
iBmpr2_CDS_1_DBJ28_R1_d19: GTTTCG_CGTACG
jKdm1a_CDS_2_DBJ28_R1_d19: CGTACG_GAGTGG
kAsh2l_3UTR_1_DBJ28_R1_d19: GAGTGG_GGTAGC
lAsh2l_CDS_2_DBJ28_R1_d19: GGTAGC_AGTCAA
mDnmt3a_CDS_2_DBJ28_R1_d19: AGTCAA_ATGAGC
nAcvr1_CDS_1_DBJ28_R1_d19: AGTTCC_ATTCCT
oGins3_CDS_1_DBJ28_R1_d19: ATGTCA_CAAAAG
pCdyl_CDS_1_DBJ28_R1_d19: CCGTCC_CAACTA
qClspn_3UTR_2_DBJ28_R1_d19: GTAGAG_CACCGG
rBrca2_CDS_1_DBJ28_R1_d19: GTCCGC_CACGAT
sBmpr2_CDS_2_DBJ28_R1_d19: GTGAAA_CACTCA
tCul3_CDS_2_DBJ28_R1_d19: GTGGCC_CAGGCG
uHdac3_3UTR_1_DBJ28_R1_d19: GTTTCG_CATGGC
vAcvr1b_CDS_1_DBJ28_R1_d19: CGTACG_CATTTT
wHdac3_CDS_2_DBJ28_R1_d19: GAGTGG_CCAACA
xCbx3_CDS_2_DBJ28_R1_d19: GGTAGC_ACTGAT
yFbxo8_CDS_1_DBJ28_R1_d19: AGTCAA_CTAGCT
zJarid2_CDS_2_DBJ28_R1_d19: AGTTCC_CTATAC
aaBmpr2_CDS_3_DBJ28_R1_d19: ATGTCA_CTCAGA
abDnmt3a_CDS_3_DBJ28_R1_d19: CCGTCC_GACGAC
acJarid2_CDS_3_DBJ28_R1_d19: GTAGAG_TAATCG
adAurka_CDS_2_DBJ28_R1_d19: GTCCGC_TACAGC
aeCul3_CDS_3_DBJ28_R1_d19: GTGAAA_TATAAT
afLUCIFERASE_CDS_4_DBJ28_R1_d19: GTGGCC_TCATTC
agAcvr1b_CDS_2_DBJ28_R1_d19: GTTTCG_TCCCGA
ahAurka_CDS_3_DBJ28_R1_d19: CGTACG_TCGAAG
aiAsh2l_CDS_3_DBJ28_R1_d19: GAGTGG_TCGGCA
ajGins3_CDS_2_DBJ28_R1_d19: GGTAGC_CGGAAT
akCbx3_CDS_3_DBJ28_R1_d19: ACTGAT_AGTTCC
alCdyl_CDS_2_DBJ28_R1_d19: ATGAGC_ATGTCA
amBrca2_CDS_2_DBJ28_R1_d19: ATTCCT_CCGTCC
anAff1_CDS_1_DBJ28_R1_d19: CAAAAG_GTAGAG
aoAcvr1_CDS_2_DBJ28_R1_d19: CAACTA_GTCCGC
apHdac3_CDS_3_DBJ28_R1_d19: CACCGG_GTGAAA
aqAcvr1b_CDS_3_DBJ28_R1_d19: CACGAT_GTGGCC
arBmpr2_CDS_4_DBJ28_R1_d19: CACTCA_GTTTCG
asGFP_CDS_4_DBJ28_R1_d19: CAGGCG_CGTACG
atCdyl_3UTR_3_DBJ28_R1_d19: CATGGC_GAGTGG
auAcvr1_CDS_3_DBJ28_R1_d19: CATTTT_GGTAGC
avClspn_3UTR_3_DBJ28_R1_d19: CCAACA_AGTCAA
awH2afy_CDS_1_DBJ28_R1_d19: ACTGAT_ATGAGC
axJarid2_CDS_4_DBJ28_R1_d19: ATGAGC_ATTCCT
ayGins3_CDS_3_DBJ28_R1_d19: ATTCCT_CAAAAG
azCbx3_3UTR_4_DBJ28_R1_d19: CAAAAG_CAACTA
baHdac3_CDS_4_DBJ28_R1_d19: CAACTA_CACCGG
bbCul3_CDS_4_DBJ28_R1_d19: CACCGG_CACGAT
bcKdm1a_CDS_3_DBJ28_R1_d19: CACGAT_CACTCA
bdBrca2_CDS_3_DBJ28_R1_d19: CACTCA_CAGGCG
beAff1_CDS_2_DBJ28_R1_d19: CAGGCG_CATGGC
bfClspn_CDS_4_DBJ28_R1_d19: CATGGC_CATTTT
bgHdac3_CDS_5_DBJ28_R1_d19: CATTTT_CCAACA
bhAcvr1_CDS_4_DBJ28_R1_d19: CCAACA_ACTGAT
biH2afy_CDS_2_DBJ28_R1_d19: ACTGAT_CTAGCT
bjCbx3_CDS_5_DBJ28_R1_d19: ATGAGC_CTATAC
bkKdm1a_CDS_4_DBJ28_R1_d19: ATTCCT_CTCAGA
blDnmt3a_CDS_4_DBJ28_R1_d19: CAAAAG_GACGAC
bmCdyl_CDS_4_DBJ28_R1_d19: CAACTA_TAATCG
bnAff1_CDS_3_DBJ28_R1_d19: CACCGG_TACAGC
boH2afy_CDS_3_DBJ28_R1_d19: CACGAT_TATAAT
bpCdyl_CDS_5_DBJ28_R1_d19: CACTCA_TCATTC
bqJarid2_3UTR_5_DBJ28_R1_d19: CAGGCG_TCCCGA
brAcvr1b_CDS_4_DBJ28_R1_d19: CATGGC_TCGAAG
bsDnmt3a_CDS_5_DBJ28_R1_d19: CATTTT_TCGGCA
btAff1_3UTR_4_DBJ28_R1_d19: CCAACA_CGGAAT
buGins3_CDS_4_DBJ28_R1_d19: CGGAAT_AGTTCC
bvAff1_CDS_5_DBJ28_R1_d19: CTAGCT_ATGTCA
bwH2afy_CDS_4_DBJ28_R1_d19: CTATAC_CCGTCC
bxAcvr1b_CDS_5_DBJ28_R1_d19: CTCAGA_GTAGAG
byBmpr2_3UTR_5_DBJ28_R1_d19: GACGAC_GTCCGC
bzFbxo8_CDS_2_DBJ28_R1_d19: TAATCG_GTGAAA
caAsh2l_CDS_4_DBJ28_R1_d19: TACAGC_GTGGCC
cbAurka_CDS_4_DBJ28_R1_d19: TATAAT_GTTTCG
ccKdm1a_CDS_5_DBJ28_R1_d19: TCATTC_CGTACG
cdAsh2l_CDS_5_DBJ28_R1_d19: TCCCGA_GAGTGG
ceFbxo8_CDS_3_DBJ28_R1_d19: TCGAAG_GGTAGC
cfFbxo8_3UTR_4_DBJ28_R1_d19: TCGGCA_AGTCAA
cgClspn_CDS_5_DBJ28_R1_d19: CGGAAT_ATGAGC
chCul3_CDS_5_DBJ28_R1_d19: CTAGCT_ATTCCT
ciFbxo8_CDS_5_DBJ28_R1_d19: CTATAC_CAAAAG
cjBrca2_3UTR_4_DBJ28_R1_d19: CTCAGA_CAACTA
ckAcvr1_CDS_5_DBJ28_R1_d19: GACGAC_CACCGG
clAurka_CDS_5_DBJ28_R1_d19: TAATCG_CACGAT
cmBrca2_CDS_5_DBJ28_R1_d19: TACAGC_CACTCA
cnGins3_3UTR_5_DBJ28_R1_d19: TATAAT_CAGGCG
coNA_NA_6_DBJ28_R1_d19: TCATTC_CATGGC
cpNA_NA_7_DBJ28_R1_d19: TCCCGA_CATTTT
cqH2afy_CDS_5_DBJ28_R1_d19: TCGAAG_CCAACA
crNA_NA_8_DBJ28_R1_d19: TCGGCA_ACTGAT
step2:
#### Additional switches:
#### Do not change these unless you know what you are doing
## MAPQ=30 is high quality threshold
minimal_MAPQ: 12
LongReadSplitPattern: A7 A6 A18 A*
ShortReadSplitPattern: A7 A6 A18 A11 A*
T2_small: TCGCTAATTGC