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Search: Posts Made By: Adamo
Forum: Bioinformatics 08-20-2010, 02:00 AM
Replies: 33
Views: 17,173
Posted By Adamo
Ok, I didn't notice you'd posted here! Thanks a...

Ok, I didn't notice you'd posted here!
Thanks a lot, I'm gonna see what's in it now.
Forum: Bioinformatics 07-19-2010, 01:22 AM
Replies: 123
Views: 46,433
Posted By Adamo
I have resolved the problem. It was caused by the...

I have resolved the problem. It was caused by the absence of the corresponding sequences of the matches in the sam file converted from psl. And as Tablet doesn't represent a read without its...
Forum: Bioinformatics 07-16-2010, 04:06 AM
Replies: 0
Views: 2,622
Posted By Adamo
Getting sequences into a bam file - psl2sam.pl

Hello,

I have a psl file, and convert it into sam format using psl2sam.pl (samtools).
I'd like to know if there is a way of getting the target sequence in the sam file in place of the "*"...
Forum: Bioinformatics 07-16-2010, 12:03 AM
Replies: 123
Views: 46,433
Posted By Adamo
Thank you anyway. This problem happens with...

Thank you anyway.

This problem happens with all the reads, not only the one mentionned. It may be psl2sam or Blat which causes this error.
Forum: Bioinformatics 07-15-2010, 11:49 PM
Replies: 123
Views: 46,433
Posted By Adamo
Hi, Tablet gives me the following error...

Hi,

Tablet gives me the following error message while trying to load a sorted bam file and its corresponding genome:

java.lang.Exception: java.lang.RuntimeException: SAM validation error:...
Forum: Bioinformatics 07-15-2010, 03:10 AM
Replies: 5
Views: 2,689
Posted By Adamo
Yes, I knew I'd not chosen the most efficient way...

Yes, I knew I'd not chosen the most efficient way to do the job... I'm not very comfortable with informatics!
Thanks kmcarr and Dethecor, I've done what you've suggested: the program now stores...
Forum: Bioinformatics 07-13-2010, 12:09 AM
Replies: 5
Views: 2,689
Posted By Adamo
[Optimization] perl script for unaligned reads

Hello,

I have intended to write a script to extract unaligned reads from a fasta file.

The script takes the first line of the file which contains all the reads, and run throught the entire one...
Forum: Bioinformatics 07-06-2010, 06:36 AM
Replies: 10
Views: 7,091
Posted By Adamo
Oops, mistake.

Oops, mistake.
Forum: Bioinformatics 07-06-2010, 06:28 AM
Replies: 10
Views: 7,091
Posted By Adamo
The thing is, I've reads of different lenghts,...

The thing is, I've reads of different lenghts, from 100bp to 300bp. Can't I specify a percentage instead of a precise score?
Forum: Bioinformatics 07-06-2010, 05:22 AM
Replies: 10
Views: 7,091
Posted By Adamo
Thanks you again, I'm having a look at your...

Thanks you again, I'm having a look at your script. It seems quite approachable, even for me!
I'll let you know if I need some more help.
Forum: Bioinformatics 07-05-2010, 12:04 AM
Replies: 10
Views: 7,091
Posted By Adamo
Thank you, I think it can be very helpful! ...

Thank you, I think it can be very helpful!

However, I have some questions about how to use the scripts (I'm all new to biology and bioinformatic...):

Why should I mask the genome? (actually, I...
Forum: Bioinformatics 07-02-2010, 12:30 AM
Replies: 9
Views: 26,660
Posted By Adamo
If you've used bwasw then the command line...

If you've used bwasw then the command line suggested by Adrian won't work.
You'll have to write your own perl or awk script to extract unmapped reads comparing your bam output with your fastq file...
Forum: Bioinformatics 06-22-2010, 07:49 AM
Replies: 23
Views: 22,672
Posted By Adamo
After further researches, it seems like bwasw...

After further researches, it seems like bwasw doesn't include any unmapped read in the output file, unlike bwa aln.
I think I might have to write a script which could handle such a job.

Thanks...
Forum: Bioinformatics 06-22-2010, 01:54 AM
Replies: 23
Views: 22,672
Posted By Adamo
I'll try the mailing list, thanks for the tip. ...

I'll try the mailing list, thanks for the tip.
I've already run bwa several times, with default parameters and followed the steps suggested by the readme. Nothing more, nothing less...

I'm quite...
Forum: Bioinformatics 06-22-2010, 01:31 AM
Replies: 23
Views: 22,672
Posted By Adamo
Well, I'm a little confused. My sam file...

Well, I'm a little confused.
My sam file contains only the reads mapped. The thing is that I read on a topic a post from lh3 (who know what he speaks about, I think!) telling someone that all the...
Forum: Bioinformatics 06-22-2010, 12:58 AM
Replies: 23
Views: 22,672
Posted By Adamo
The first lines of my sam file are: My...

The first lines of my sam file are:



My command is:



I also tried -bt instead of -bT (replacing db.fa by db.fa.fai (I indexed my database with samtools faidx)) but the result is just the...
Forum: Bioinformatics 06-22-2010, 12:09 AM
Replies: 23
Views: 22,672
Posted By Adamo
I think the command's ok but still, I have no...

I think the command's ok but still, I have no read in the output file. I don't get it!
I have only about 2% of mapped reads in my .sam file according to flagstat...
I've tried both commands you...
Forum: Bioinformatics 06-21-2010, 01:46 AM
Replies: 23
Views: 22,672
Posted By Adamo
I have resolved the problem concerning the error...

I have resolved the problem concerning the error message, thanks.
But for the other one, I'm still try to figure out where the problem is.
I've tried your command (btw, I didn't paste perfectly...
Forum: Bioinformatics 06-17-2010, 05:17 AM
Replies: 10
Views: 7,091
Posted By Adamo
Yes, "most likely to be true" is a very fuzzy...

Yes, "most likely to be true" is a very fuzzy notion here.
I hadn't see pslReps/Sort... was distributed with blast, I'm still a newbie and I'm quite confused with all the different softs that have...
Forum: Bioinformatics 06-17-2010, 12:05 AM
Replies: 23
Views: 22,672
Posted By Adamo
BWA - unmapped reads

Hello everyone,

I'm trying to combine the use of bwa and blat but I have a few difficulties to extract the unmapped reads from bwa.
It appears they are in the first .sam file created using bwa...
Forum: Bioinformatics 06-16-2010, 11:57 PM
Replies: 10
Views: 7,091
Posted By Adamo
BLAT - uniquely mapped reads/multiple hits

Hi all,

I wanted to know if there was a simple way to filter the output.psl from BLAT to obtain a file containing only the uniquely mapped reads.
Concerning the multiple hits, does BLAT sort them...
Forum: Bioinformatics 06-14-2010, 05:47 AM
Replies: 8
Views: 4,594
Posted By Adamo
Ok, I didn't know how a BAM file worked... I...

Ok, I didn't know how a BAM file worked... I understand now, sorry for the question.
I'll follow your advices. An ACE file seems appropriate for the data i'm interested in.
Forum: Bioinformatics 06-14-2010, 01:04 AM
Replies: 8
Views: 4,594
Posted By Adamo
I have a few questions... It seems like the...

I have a few questions...
It seems like the soft only take into account the reads that map with the part of genome in the area of the viewing bar. Can I change it so that all the reads that map with...
Forum: Bioinformatics 06-13-2010, 11:57 PM
Replies: 8
Views: 4,594
Posted By Adamo
I'll give it a try, thanks.

I'll give it a try, thanks.
Forum: Bioinformatics 06-13-2010, 11:41 PM
Replies: 8
Views: 4,594
Posted By Adamo
Visualizing with samtools?

Hi,

I have some difficulties in manipulating BWA and samtools.
I have sorted my alignment stored in the .bam file, and indexed it (so I have a .bma and a .bam.bai).
To visualize the sequences,...
Showing results 1 to 25 of 28

 


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