How to get unique mapped with TAMP?

[gigigou]

Hi ,all.

I'm using TMAP to align Ion Torrent reads. I wonder how I can get unique mapped reads from the TMAP output SAM files.

I find the -a parameter, it seems that to set -a 0 will produce unique map. But from the description I think that -a 0 means if there are multiple alignments TMAP will chose the one with best score, obviously this is not unique.

So if anyone can help me with this?

Many thanks!

[Michael.Ante]

Hi gigigou,

After running TMAP you have to count the mapped reads which mapped only once.
One straight-forward (but maybe inefficient) approach is to count them with awk on the command line:

samtools view tmap.sort.bam | awk '!match($3,/\*/){t[$1]++}END{for(i in t){if(t[i]==1){print i}}}'

This will give you a list of read-IDs which aligned to a chromosomal location (field 3 must not be '*') and occured only once. You can use this list to filter your bam/sam-file.

I hope this will help you.

[gigigou]

Hi gigigou,

After running TMAP you have to count the mapped reads which mapped only once.
One straight-forward (but maybe inefficient) approach is to count them with awk on the command line:

samtools view tmap.sort.bam | awk '!match($3,/\*/){t[$1]++}END{for(i in t){if(t[i]==1){print i}}}'

This will give you a list of read-IDs which aligned to a chromosomal location (field 3 must not be '*') and occured only once. You can use this list to filter your bam/sam-file.

I hope this will help you.

Thank you!

I'll try it and tell you if it works!

Many thanks.