I used the default bowtie method for rsem-calculate-expression but I had problems determining the number of reads in the resulting BAM file. I did some investigating and found that the reason is the read IDs have different numbers of fields for the first and second reads of a read pair. For example,
Hi @DarioS , we are aware of this behavior of Bowtie. If you update to the latest version of RSEM, RSEM will extract the canonical read name (with strings after spaces discarded).
I used the default bowtie method for
rsem-calculate-expression
but I had problems determining the number of reads in the resulting BAM file. I did some investigating and found that the reason is the read IDs have different numbers of fields for the first and second reads of a read pair. For example,The extra
2:N:0:GTCCGC
is only kept for second reads, but not for first. Could this be consistent for both pairs of reads?I also mapped this data with STAR to the genome and the BAM file has consistent naming formats of all the read IDs.