output files are empty except fromGTF...txt files. Help! --__--
72 views
Skip to first unread message
罗浩迪
Mar 26, 2023, 4:10:44 AM3/26/23
to rMATS User Group
rmats（version:4.1.2）bam files from bowtie2
kutsc...@gmail.com
Mar 28, 2023, 9:21:20 AM3/28/23
to rMATS User Group
The issue is that all the reads were NOT_NH_1:
USED: 0
NOT_NH_1: 122279800
total: 122279800
rMATS requires the NH tag, but it looks like bowtie2 does not use the NH tag: https://github.com/BenLangmead/bowtie2/issues/200
USED: 0
NOT_NH_1: 122279800
total: 122279800
rMATS requires the NH tag, but it looks like bowtie2 does not use the NH tag: https://github.com/BenLangmead/bowtie2/issues/200
You could realign your reads with STAR which does use the NH tag. Or you could manually edit your bam files and add NH:i:1 for each alignment
Eric
Reply all
Reply to author
Forward
0 new messages