Question: Read counts at specific locations in SAM files
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gravatar for fogarty.mc
8 months ago by
fogarty.mc0
fogarty.mc0 wrote:

I have sam files created using hisat2 of RNAseq reads assembled to a reference of 7 genes (not whole genome). What I need to be able to do is for a given position in the assembly I need too: 1. Count the total # of reads at that position 2. Count of reads of each nucleotide at that position

I have ~30 Rnaseq libraries and ~70 positions I need to assay. This was done in a allohexaploid species so I am looking at positions know to be polymorphic between genomes.

Any ideas of how best to do this?

hisat2 rna-seq sam • 222 views
ADD COMMENTlink written 8 months ago by fogarty.mc0

bam-readcount will do this for you. Samtools depth/mpileup would be other options.

ADD REPLYlink written 8 months ago by genomax74k
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