Incompatibility with masked reference genomes
See original GitHub issueIncompatibility with masked reference genomes
call-macs2
fails if a masked reference (where Ns are used to indicate repetitive regions) is used to build a custom genome reference database.
run_shell_cmd: PID=70151, CMD=bedtools intersect -a ${SAMPLE}.trim.merged.nodup.tn5.tagAlign.tmp1 -b ${SAMPLE}.trim.merged.nodup.tn5.pval0.01.300K.bfilt.narrowPeak.tmp2 -wa -u | wc -l
Traceback (most recent call last):
File "/users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/bin/encode_macs2_atac.py", line 210, in <module>
main()
File "/users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/bin/encode_macs2_atac.py", line 200, in main
frip_qc = frip( args.ta, bfilt_npeak, args.out_dir)
File "/users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/bin/encode_frip.py", line 54, in frip
write_txt(frip_qc, str(float(val1)/float(val2)))
ValueError: could not convert string to float: ***** WARNING: File rat_liver7_S12_L001_R1_001.trim.merged.nodup.tn5.tagAlign.tmp1 has inconsistent naming convention for record:
AABR07024382.1 100568 100639 N 1000 +
If it would be impractical to include compatibility with masked references, it would be helpful to specify that the pipeline is incompatible with masked references in the documentation. I understand that this is the function of the blacklist input, but blacklisted regions can be more difficult to define for less popular model organisms.
Issue Analytics
- State:
- Created 5 years ago
- Comments:9 (2 by maintainers)
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This is actually a duplicate issue of #48 and will be fixed in the next release.
Interesting. This is a bug/unintended behavior so we’d like to get to the bottom of it. I’ll ask @leepc12 to get in touch with you so we can get to the bottom of it and fix the issue.
On Sat, Nov 3, 2018, 12:05 PM nicolerg <notifications@github.com wrote: