Entering edit mode
6.6 years ago
abhijit.synl
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60
Hello All,
I have a standard SAM output from the HISAT2 splice aware aligner. I want to add the Query hit index tag to the output, which indicates position of the alignment record in SAM file. Is there a way to do that? The dataset is 50 bp SE RNA-Seq reads mapped to the genome using HISAT2
Thank you Abhijit
Could you post the results of:
And:
edit: by the way, why do you want the query hit index?
I want to use the program TransComb. It needs Tophat2 output with the Hit Query index field. Hisat2 does not give that. Here is the output. I am masking the reads cuz data is proprietary