Forcing alignment only to the forward reference for HISAT-3N

DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)

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Forcing alignment only to the forward reference for HISAT-3N #398

Open cahn20 opened 1 year ago

cahn20 commented 1 year ago

Hello,

I've performed alignment using HISAT-3N to get the following results:

Is there a method to force alignment of paired-end RNA-seq data only to the forward strand? I don't want any alignment to "mmu-mir-122b" shown in the figure above (which is one of the many examples I've seen).

Is the "--norc" option for something else? Using the "--norc" option doesn't seem to prevent alignment to the reverse reference. Thanks a lot in advance.

imzhangyun commented 1 year ago

Hello Chris,

Sorry the HISAT-3N disabled the --nofw and --norc function. To get the alignment results only mapped to FW strand, please use samtools. samtools view -F 0x10 should help you filter the alignment result.

Best, Leo