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leepc12 avatar leepc12 commented on July 28, 2024 1

Chromosome names in two files (tss_enrich and chrsz) don't match.
Your chrsz file looks like.

$ cat rn6_masked.chrom.sizes.txt | head
1       282763074
2       266435125
3       177699992
4       184226339
5       173707219
6       147991367
7       145729302
8       133307652
9       122095297
10      112626471

Your tss file.

$ zcat tss.rn6.bed.gz  | head
chr1    100037072       100037073       ENSRNOG00000048901      0       +
chr1    100047235       100047236       ENSRNOG00000045980      0       +
chr1    100059967       100059968       ENSRNOG00000032857      0       +
chr1    100086520       100086521       ENSRNOG00000032857      0       +
chr1    100131449       100131450       ENSRNOG00000032857      0       +
chr1    100131562       100131563       ENSRNOG00000032857      0       +
chr1    100161872       100161873       ENSRNOG00000033414      0       +
chr1    100164400       100164401       ENSRNOG00000054979      0       +
chr1    100189515       100189516       ENSRNOG00000033805      0       +
chr1    100199057       100199058       ENSRNOG00000032857      0       +

from atac-seq-pipeline.

nicolerg avatar nicolerg commented on July 28, 2024

Are new versions tested with sample data before being committed? I've been submitting bugs related to non-conventional chromosome names for 6 weeks now and have not been able to get a sample to run to completion.

from atac-seq-pipeline.

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