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Forum: Bioinformatics 06-07-2016, 09:28 AM
Replies: 0
Views: 1,147
Posted By mhgseq
How to extract sequence from multiple position in sorted bam files

Hi All,

My research need to extract sequence from multiple position in sorted bam files.
I have the bam files sorted. I would like to extract and keep sequence from multiple positions according...
Forum: Ion Torrent 04-28-2016, 08:36 AM
Replies: 8
Views: 8,208
Posted By mhgseq
thanks a lot. Your heat cooled approach works...

thanks a lot. Your heat cooled approach works well. We get much better reads this time.
Forum: Ion Torrent 04-20-2016, 09:16 AM
Replies: 8
Views: 8,208
Posted By mhgseq
We do check the bioanalyzer, not a lot of large...

We do check the bioanalyzer, not a lot of large size shift. But we do see a lots of small variation in size (our amplicon is about 200bp (include primer and adaptor), we do see peak at 180-250bp in...
Forum: Ion Torrent 04-19-2016, 04:46 PM
Replies: 8
Views: 8,208
Posted By mhgseq
Thank you so much for the info. I am also do the...

Thank you so much for the info. I am also do the similar short amplicon ( ~100bp + primers+ adaptor). But for the loading, we load much higher concentration for OT2 (200 pM vs the recommend 26 pM), I...
Forum: Ion Torrent 04-19-2016, 03:07 PM
Replies: 8
Views: 8,208
Posted By mhgseq
Have you solve your probelm of <60bp short reads....

Have you solve your probelm of <60bp short reads.

I have similar problem with my fusion primer amplicon seq with Ion Torrent. Everything is fine in last several month with up to 16 barcode. When...
Forum: Bioinformatics 10-14-2015, 08:08 AM
Replies: 679
Views: 215,649
Posted By mhgseq
Thank you very much. After specify K in both...

Thank you very much. After specify K in both command, it works.
Forum: Bioinformatics 10-13-2015, 03:35 PM
Replies: 679
Views: 215,649
Posted By mhgseq
out of memory error

even with a very small ref and input file, I got the out of memory error. Would you check what is happen?


bbmap.sh in=~/Documents/align/test.fa out=~/Documents/align/outputu.sam

java...
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