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Forum: Bioinformatics 06-27-2011, 09:46 AM
Replies: 1
Views: 2,019
Posted By AnamikaDarwin
Question Evidence of Strand Bias

Hello,


For my SNP positions, I am getting count of reads that are each on the forward and reverse strands. If there were no strand bias one expects the ratio of these counts to be centered...
Forum: Bioinformatics 01-22-2010, 06:53 AM
Replies: 0
Views: 1,769
Posted By AnamikaDarwin
Question SNP Caller for BAM Files

Have people used other tools apart from Samtools' SNP caller for calling SNPs? If yes, how does it compare?

Cheers,
AnamikaD
Forum: Bioinformatics 07-24-2009, 09:00 AM
Replies: 0
Views: 1,110
Posted By AnamikaDarwin
maq 2nd and 3rd likely SNP Calls

Hello,

I use the maq snp caller for snp calling on a diploid organism. The filtered maq snp report gives the most likely, 2nd likely and the 3rd likely calls.

Does anybody consider 2nd and 3rd...
Forum: Bioinformatics 07-24-2009, 08:43 AM
Replies: 14
Views: 7,413
Posted By AnamikaDarwin
Question Hello qqcandy, I came across your posting...

Hello qqcandy,

I came across your posting from 10 months ago and I am wondering if you have resolved the issue? If yes, how did you do it?

I am using maq to find snps and for most part get...
Forum: Bioinformatics 06-29-2009, 01:44 PM
Replies: 2
Views: 5,048
Posted By AnamikaDarwin
Hi Xiang, My issue got resolved after I...

Hi Xiang,

My issue got resolved after I indexed the reference assembly by running the command samtools faidx ref.fasta.

~Anamika
Forum: Bioinformatics 06-13-2009, 04:01 PM
Replies: 5
Views: 4,131
Posted By AnamikaDarwin
Hi Chipper, I changed the default values...

Hi Chipper,

I changed the default values for all the gap parameters -o, -O & -E. I get marginally more alignments, but still the depth is quite low.

~ Mika
Forum: Bioinformatics 06-12-2009, 04:15 PM
Replies: 5
Views: 4,131
Posted By AnamikaDarwin
Hello Heng, I took your advice on using BWA...

Hello Heng,

I took your advice on using BWA for helicos data. Since helicos does not have inherent quality scores associated with it, I simulated and gave "perfect" scores for all the reads. In...
Forum: Bioinformatics 05-22-2009, 11:52 AM
Replies: 0
Views: 1,891
Posted By AnamikaDarwin
Question Run maq on solexa data with simulated qual scores

Hello,

I have single-end solexa reads, wherein the qual scores are the same for every base. I would like to be able to run maq map on this data. With the default options, I am not getting any...
Forum: Bioinformatics 04-29-2009, 10:33 AM
Replies: 2
Views: 5,048
Posted By AnamikaDarwin
Question Samtools Pileup Assertion Error

Hello,

I am trying to use the samtools pileup command with the -c and -f flags to get the consensus sequnce, but am getting an error.

Command : samtools pileup -c -f RefAssemb.fasta...
Forum: Bioinformatics 04-27-2009, 08:45 AM
Replies: 2
Views: 2,986
Posted By AnamikaDarwin
Question BWA Paper

Hello,

Does anyone have a link to the BWA paper?

Thanks,
Anamika
Forum: Bioinformatics 04-21-2009, 11:57 AM
Replies: 5
Views: 4,131
Posted By AnamikaDarwin
Question Helicos

Hello,

Is it possible to use MAQ for helicos reads?

Thanks,
Anamika
Forum: Bioinformatics 04-10-2009, 07:27 AM
Replies: 1
Views: 2,992
Posted By AnamikaDarwin
Question BWA Read Length

Hello,

What is the maximum read length that can be used in BWA?

Thanks,
Anamika
Forum: Bioinformatics 03-13-2009, 06:22 AM
Replies: 3
Views: 1,347
Posted By AnamikaDarwin
swbarnes, This I am aware of. However, in...

swbarnes,

This I am aware of. However, in maqview, on the same read I have a combination of upper and lower case letters.

Thanks!
Anamika
Forum: Bioinformatics 03-12-2009, 04:13 PM
Replies: 3
Views: 1,347
Posted By AnamikaDarwin
Question maqview upper and lower case

Hello,

What is the difference between lower case vs upper case letters are in the maq viewer?

From the maq manual, for the command maq cns2fq it states "bases in lower case are essentially...
Forum: Bioinformatics 03-06-2009, 06:50 AM
Replies: 50
Views: 15,583
Posted By AnamikaDarwin
Question maqview freeglut error

Hello,

I am having similar issues like other users, i.e. get the following error message:

maqview s512.3diff.mapMerge
freeglut /maqview/bin/maqview: relocation error: /maqview/bin/maqview:...
Forum: Bioinformatics 03-03-2009, 08:53 AM
Replies: 11
Views: 3,187
Posted By AnamikaDarwin
Hi Zee, I use the option you suggest to get...

Hi Zee,

I use the option you suggest to get the read depth for the SNP data. However, my aim is to get those coordinates of the assembly that did not align with my input reads. I have about ~15%...
Forum: Bioinformatics 03-03-2009, 08:41 AM
Replies: 0
Views: 955
Posted By AnamikaDarwin
Question maq mapcheck

Hello,

I have been using maq to align illumina reads to a reference assembly. I am using maq mapcheck to get the read statistics.

I have a question about the section that reports the depth and...
Forum: Bioinformatics 02-21-2009, 01:38 PM
Replies: 11
Views: 3,187
Posted By AnamikaDarwin
Thumbs up maq mapview right solution

Thanks Eco. Once I ran it with the -b option ( the read sequence and the quality are not displayed).

From this output, I plan to get the coordinates of those regions that did not align (roughly...
Forum: Bioinformatics 02-21-2009, 12:43 PM
Replies: 11
Views: 3,187
Posted By AnamikaDarwin
Question Maq Alignment Coordinates

I have used maq to align a set of illumina reads to a reference assembly. Is there a way to directly get the alignment coordinates for the reference assembly?

Thanks,
Anamika

PS, I had...
Forum: Bioinformatics 01-07-2009, 10:07 AM
Replies: 5
Views: 2,719
Posted By AnamikaDarwin
Hi kwebb, Thanks for your reply. I am aware...

Hi kwebb,

Thanks for your reply. I am aware of this option. But since, I am looking for read statistics in a given window size, this information is not very useful for me.

I plot the alignment...
Forum: Bioinformatics 01-07-2009, 07:48 AM
Replies: 5
Views: 2,719
Posted By AnamikaDarwin
Question MAQ Alignment Depth

Hello,

Is it possible to get the alignment depth after one aligns with maq map? I want to compute how many reads align for a defined window size?

Thanks,
Anamika.
Forum: Bioinformatics 12-15-2008, 01:35 PM
Replies: 4
Views: 2,246
Posted By AnamikaDarwin
Thanks Stegger, I AM looking to getting an...

Thanks Stegger,

I AM looking to getting an overview of of SOLEXA read qualities. I would like to be able to discern the qualities of those reads that are aligning with my reference using MAQ.
...
Forum: Bioinformatics 12-15-2008, 01:32 PM
Replies: 5
Views: 4,018
Posted By AnamikaDarwin
Question MAQ Scores & Quantify maq alignments?

Hello,

Is there a way to discern how well reads are aligning to a reference assembly using the mapping quality scores?

Thanks,
AnamikaDarwin
Forum: Bioinformatics 12-12-2008, 12:44 PM
Replies: 4
Views: 2,246
Posted By AnamikaDarwin
Question Assess the quality of solexa reads

Hello,

How can you assess the quality of solexa reads?

Thanks,
AnamikaDarwin
Forum: Bioinformatics 11-23-2008, 08:01 AM
Replies: 1
Views: 2,843
Posted By AnamikaDarwin
Question maq map - Assertion 'matches' failed

Hello,

I am running maq 0.7.1. When I run the maq map command with the following options:
maq map -m 0.005 -n 2 -u s512a.poor.unmap -H s512a.multiple.mismatch My.bfa s51a.bfq s52a.bfq

I am...
Showing results 1 to 25 of 26

 


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