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Hi,
I'm using gsnap to align RNA reads against a reference genome. I used the option --pairmax-rna=300 but it seems it doesn't work in the SAM output provided by gsnap.
For example, a read pair aligned with a detected insert length of 745 bp, using --pairmax-rna=300, is well aligned in the gsnap output (reads tagged as "paired" and "toolong") but the same reads in the SAM file have a SAM flag of 99/147 instead of 97/145.
Does any one have an idea about that ?
Other question, do you know the difference between --pairmax-rna and --pairmax ?
Thanks
I'm using gsnap to align RNA reads against a reference genome. I used the option --pairmax-rna=300 but it seems it doesn't work in the SAM output provided by gsnap.
For example, a read pair aligned with a detected insert length of 745 bp, using --pairmax-rna=300, is well aligned in the gsnap output (reads tagged as "paired" and "toolong") but the same reads in the SAM file have a SAM flag of 99/147 instead of 97/145.
Does any one have an idea about that ?
Other question, do you know the difference between --pairmax-rna and --pairmax ?
Thanks