SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 4 of 4
Search took 0.00 seconds.
Search: Posts Made By: Oyster
Forum: Bioinformatics 09-01-2012, 01:07 PM
Replies: 0
Views: 1,009
Posted By Oyster
bowtie - reads aligned does not match reported alignments

Hi,

A bowtie question of output interpretation,

CMD:

bowtie -p 16 -a --best --strata -q -S --sam-nohead -q -v 2 target single_dir/single_fa > single_dir/single_fa.pre.sam

STDERR:
Forum: Bioinformatics 03-15-2011, 09:44 AM
Replies: 9
Views: 17,963
Posted By Oyster
yes i do have their number

I have not succeeded in grabbing the +3000 sequences from my +35 million sequences.

If you know a way, please do share.

Thanks
Forum: Bioinformatics 03-14-2011, 01:38 PM
Replies: 9
Views: 17,963
Posted By Oyster
Thanks kmcarr. Indeed, that post was exactly...

Thanks kmcarr. Indeed, that post was exactly what I needed, yet I remain with a couple of questions.

'makeblastdb' with the '-parse_seqids' option seems like way to go to do this task.
...
Forum: Bioinformatics 03-11-2011, 09:28 AM
Replies: 9
Views: 17,963
Posted By Oyster
extract full fasta file for local blast hits

Hi all,

I would like to take local blast hit sequences, i.e. hsp_hseq in blast xml
format, and extract the full sequences of those hits from the original fasta
file (as the xml output only...
Showing results 1 to 4 of 4

 


All times are GMT -8. The time now is 06:24 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO