Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
multiple read mapping with the same read set with newbler vincebaby6 Bioinformatics 6 12-20-2012 03:10 AM
Tophat 2.0.5 mixed length reads - how to set MID dvanic Bioinformatics 0 10-02-2012 08:16 PM
picard error: Mismatch between read length and quals length writing read shawpa Bioinformatics 0 08-20-2012 06:52 AM
Tmap: how to use it to construct genetic map with large-scale SNP markers orctyr Bioinformatics 0 03-16-2011 02:11 AM
how to set seed length in Tophat sanwen Bioinformatics 2 08-10-2010 01:07 AM

Thread Tools
Old 11-11-2013, 04:58 PM   #1
Junior Member
Location: Hungary

Join Date: Nov 2013
Posts: 1
Question 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,

Last edited by kadri; 11-12-2013 at 02:48 AM.
kadri is offline   Reply With Quote

ion torrent, proton, read length varies, tmap

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:05 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO