tmap - set up read length to map?

kadri · 11-11-2013, 04:58 PM

Hello All,

I would really appreciate if somebody could help me. I use this command to run tmap on the Ion Torrent server:

tmap mapall -n 12 -s <outputfile.bam> -f <fastafile> -r <bamfile> -v -Y -u -o 1 stage1 map4

(and I also use samtools sort and index prompts to map my reads).

I am really satisfied with it, works nicely

I would like to change my command to be able to specify the length of the mapped reads. I need them to overlap a certain part in my reference sequence, so I am interested only those which are theoretically long enough to overlap this part of the sequence. I red in the t-map book, that there is a parameter map1 -l INT, but I am not sure how to use it. I have already tried several ways to add it into my original command, but it did not work. So do you have any idea how to change my command?

Thanks a lot.
Kind Regards,
Adrienn

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11-11-2013, 04:58 PM	#1
kadri Junior Member Location: Hungary Join Date: Nov 2013 Posts: 1	tmap - set up read length to map? Hello All, I would really appreciate if somebody could help me. I use this command to run tmap on the Ion Torrent server: tmap mapall -n 12 -s <outputfile.bam> -f <fastafile> -r <bamfile> -v -Y -u -o 1 stage1 map4 (and I also use samtools sort and index prompts to map my reads). I am really satisfied with it, works nicely I would like to change my command to be able to specify the length of the mapped reads. I need them to overlap a certain part in my reference sequence, so I am interested only those which are theoretically long enough to overlap this part of the sequence. I red in the t-map book, that there is a parameter map1 -l INT, but I am not sure how to use it. I have already tried several ways to add it into my original command, but it did not work. So do you have any idea how to change my command? Thanks a lot. Kind Regards, Adrienn Last edited by kadri; 11-12-2013 at 02:48 AM.