I am using bowtie version 1.1.1 for small RNA sequencing analysis. When using the -m setting to allow multi mapping, I am not getting an -NH tag in the resulting sam file and I think this is then causing me issues when I am trying to run featurecounts with the --fraction option (which relies on the -NH tag to fraction the counts). The reason I think this is because my featurecounts raw counts are not decimal numbers, and because taking out the --fraction parameter doesn't seem to change the number of counts.
My original bowtie command was:
bowtie -v 1 -m 10 -S -a --best --strata
and subsequent featurecounts command:
featureCounts -T 16 -M -t miRNA --fraction -g ID -s 1 -F GTF -a
I have tried editing the bowtie command to take out the -a, the --best --strata and change the -m but I am still not getting an -NH tag outputted in my sam files. I do get the following types of tags:
XA:i:1 MD:Z:5T12 NM:i:1
Any insight would be really appreciated!
Thank you
Emma
Hello,
I am using bowtie version 1.1.1 for small RNA sequencing analysis. When using the -m setting to allow multi mapping, I am not getting an -NH tag in the resulting sam file and I think this is then causing me issues when I am trying to run featurecounts with the --fraction option (which relies on the -NH tag to fraction the counts). The reason I think this is because my featurecounts raw counts are not decimal numbers, and because taking out the --fraction parameter doesn't seem to change the number of counts.
My original bowtie command was: bowtie -v 1 -m 10 -S -a --best --strata
and subsequent featurecounts command: featureCounts -T 16 -M -t miRNA --fraction -g ID -s 1 -F GTF -a
I have tried editing the bowtie command to take out the -a, the --best --strata and change the -m but I am still not getting an -NH tag outputted in my sam files. I do get the following types of tags: XA:i:1 MD:Z:5T12 NM:i:1
Any insight would be really appreciated! Thank you Emma