SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 9 of 9
Search took 0.00 seconds.
Search: Posts Made By: history_of_robots
Forum: Bioinformatics 12-13-2012, 07:29 PM
Replies: 0
Views: 1,435
Posted By history_of_robots
Can Bowite2 do ungapped local alignments without mismatches?

Hello,

I am trying to make use of --local mode of Bowtie2, and I am looking for best possible alignments without gaps and mismatches.

There seem to be no option that explicitly controls the...
Forum: Bioinformatics 02-05-2012, 07:37 PM
Replies: 1
Views: 1,627
Posted By history_of_robots
Can bowtie align mates individually if they don't match?

Hello,

I am trying to use Bowtie for paired end read alignment, using SAM as the output format. If mates align within a specified insert size on the same chromosome, then alignments of two mates...
Forum: Bioinformatics 02-02-2012, 01:09 AM
Replies: 3
Views: 2,033
Posted By history_of_robots
Thanks very much, this explains the described...

Thanks very much, this explains the described behavior exactly, as indeed the reads with many mismatches end with ...########## quality scores.

However, what does make it necessary to actually...
Forum: Bioinformatics 02-02-2012, 12:10 AM
Replies: 3
Views: 2,033
Posted By history_of_robots
Does bowtie aling with > 3 mismateches?

Hello,

I run bowtie without specifying a limit on mismatches:

bowtie -p 16 --chunkmbs 1024 --phred33 --fr --all --maxins 1000 ./mm9 -1 mate1.fastq -2 mate2.fastq fr.bwt

When I examined the...
Forum: Bioinformatics 07-05-2011, 04:49 PM
Replies: 1
Views: 2,486
Posted By history_of_robots
Bowtie optional fields in SAM question

Hello,

I am unsure of how to interpret XM:i:1 in SAM as produced by Bowtie. In Bowtie manual (http://bowtie-bio.sourceforge.net/manual.shtml#sam-bowtie-output) it says:

"XM:i:<N> For a read...
Forum: Bioinformatics 07-04-2011, 12:59 AM
Replies: 3
Views: 1,700
Posted By history_of_robots
BWA on raw sequences?

Hi guys,

I previously run Bowtie on short read sequences in raw format (i.e. one sequence per lane with no other lines in the file). I want to compare the alignment by Bowtie to BWA. I looked...
Forum: Bioinformatics 07-03-2011, 09:00 PM
Replies: 10
Views: 5,388
Posted By history_of_robots
Oh cool, you are absolutely right! That's the...

Oh cool, you are absolutely right! That's the right option to index a genome for short read alignment. Thanks very much.
Forum: Bioinformatics 07-03-2011, 07:39 PM
Replies: 10
Views: 5,388
Posted By history_of_robots
You are suggesting to use '-a bwtsw'. On BWA...

You are suggesting to use '-a bwtsw'. On BWA manual (http://bio-bwa.sourceforge.net/bwa.shtml) it says: "BWA-SW can also be used to align ~100bp reads, but it is slower than the short-read...
Forum: Introductions 05-30-2011, 12:00 PM
Replies: 0
Views: 843
Posted By history_of_robots
Bon jorno.

Hello everyone!

This forum looks like a great place, I am very glad that I came across SEQanswers in an RNA-seq review (PMID:19015660)

I did a fair bit of microarray data analysis before...
Showing results 1 to 9 of 9

 


All times are GMT -8. The time now is 03:26 PM.


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