SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 27
Search took 0.00 seconds.
Search: Posts Made By: sowmyai
Forum: Bioinformatics 02-09-2017, 10:14 AM
Replies: 18
Views: 15,768
Posted By sowmyai
Looks like Jim Robinson had it backwards for the...

Looks like Jim Robinson had it backwards for the color legends. Actually

red=positive,
blue=negative

He has clarified here:
https://groups.google.com/forum/#!topic/igv-help/YiVzwnUuOZM
Forum: Bioinformatics 05-05-2014, 06:01 PM
Replies: 1
Views: 1,626
Posted By sowmyai
How does BWA identify PCR duplicates correctly?

Does it use the usual "same-start-position-for-both-paired-ends" approach? If so, why do many users do this check manually or use picard and the like to do this check instead of just filtering by...
Forum: Bioinformatics 04-18-2014, 09:13 AM
Replies: 8
Views: 2,429
Posted By sowmyai
What about the JASPAR web site? There is a...

What about the JASPAR web site? There is a "Download" button that should give you exactly the file you are looking for (unless I am misunderstanding)

http://jaspar.genereg.net

PFMs are in...
Forum: Bioinformatics 04-18-2014, 08:39 AM
Replies: 8
Views: 2,429
Posted By sowmyai
You might want to check out FIMO in the MEME...

You might want to check out FIMO in the MEME suite of tools.

http://meme.nbcr.net/meme/fimo-intro.html
Forum: Bioinformatics 04-13-2014, 02:40 PM
Replies: 3
Views: 1,059
Posted By sowmyai
Here is our GR paper that might have some answers...

Here is our GR paper that might have some answers
http://genome.cshlp.org/content/22/9/1798.long
Forum: Bioinformatics 07-16-2010, 09:42 AM
Replies: 366
Views: 204,500
Posted By sowmyai
I have sent you an email with the reports. Thank...

I have sent you an email with the reports. Thank you for taking the time to explain.
Forum: Bioinformatics 07-16-2010, 09:10 AM
Replies: 366
Views: 204,500
Posted By sowmyai
I was not so much concerned about the pass/fail...

I was not so much concerned about the pass/fail from the software.

When I say "Passed the Per Sequence quality test" I meant that the histogram peaks very steeply at 34. How can most reads have...
Forum: Bioinformatics 07-16-2010, 08:54 AM
Replies: 366
Views: 204,500
Posted By sowmyai
Thanks. In that case, I don't understand how...

Thanks.

In that case, I don't understand how my data could fail the Per Base sequence test(miserably at that - the blue line dips sharply after 35 bp - these are 76 bp reads) and pass the "Per...
Forum: Bioinformatics 07-16-2010, 08:42 AM
Replies: 366
Views: 204,500
Posted By sowmyai
Thanks very much. I am a newbie to NGS, so please...

Thanks very much. I am a newbie to NGS, so please bear with me. I apologize if my questions are too basic.

How is the "Per Sequence Quality" calculated ? Is it an average of the quality of each...
Forum: Bioinformatics 07-16-2010, 08:10 AM
Replies: 366
Views: 204,500
Posted By sowmyai
Also, what could be the reason for a dataset...

Also, what could be the reason for a dataset passing the "Per sequence Quality Score" test and failing the "Per base sequence quality" test ?
Forum: Bioinformatics 07-16-2010, 08:06 AM
Replies: 366
Views: 204,500
Posted By sowmyai
Sounds like a great tool. Thanks. I am going...

Sounds like a great tool. Thanks. I am going through the documentation before trying it and I agree with Martin that it would be great to label the X and Y axes.

On that note, could you please...
Forum: Bioinformatics 07-16-2010, 07:21 AM
Replies: 2
Views: 3,232
Posted By sowmyai
I think this is a feature rather than a problem. ...

I think this is a feature rather than a problem.
All my reads are usually written out to the SAM output by Bowtie, and the next step in my pipeline is to weed out reads that did not map by looking...
Forum: Bioinformatics 07-15-2010, 07:13 AM
Replies: 14
Views: 8,109
Posted By sowmyai
I believe you use bwa aln -n 2 ...

I believe you use bwa aln -n 2

http://bio-bwa.sourceforge.net/bwa.shtml
Forum: Bioinformatics 07-14-2010, 07:09 AM
Replies: 2
Views: 7,051
Posted By sowmyai
Anyone ? Or maybe reference to someplace I can...

Anyone ? Or maybe reference to someplace I can get the answers from ?
Forum: Bioinformatics 07-13-2010, 08:22 AM
Replies: 2
Views: 7,051
Posted By sowmyai
bwa index option bwtsw

I am having a hard time understanding the bwtsw option in bwa index command.

1. What does this do that is different from the is option and why is it recommended for longer (>10 MB) reference...
Forum: Bioinformatics 07-11-2010, 06:38 PM
Replies: 5
Views: 4,142
Posted By sowmyai
Thanks guys. Sorry foreignman, I missed the RNAME...

Thanks guys. Sorry foreignman, I missed the RNAME part of your reply.
Forum: Bioinformatics 07-07-2010, 08:10 AM
Replies: 5
Views: 4,142
Posted By sowmyai
Thank you. But that is for QNAME and FLAG, the...

Thank you. But that is for QNAME and FLAG, the first and second fields. I am talking about RNAME, the third field, which is supposed to contain the name of the reference sequence that the read mapped...
Forum: Bioinformatics 07-06-2010, 12:23 PM
Replies: 5
Views: 4,142
Posted By sowmyai
SAM tools output question

Column 3 in SAM output format is supposed to be "the name of the reference sequence where alignment occurs" - as per documentation.
If I see an asterisk (*) in column 3, what does that indicate ?...
Forum: Bioinformatics 04-30-2010, 10:12 AM
Replies: 4
Views: 2,543
Posted By sowmyai
Hello Nick I am looking for a similar...

Hello Nick

I am looking for a similar solution. Did you happen to come across anything helpful ?

Sowmya
Forum: Bioinformatics 03-24-2010, 11:29 AM
Replies: 0
Views: 1,266
Posted By sowmyai
Ploidy in Maq and SAMtools

I am working on sequencing a haploid viral genome. Maq seems to default to diploid and I am not sure about Bowtie/SAMtools.

How do I specify ploidy in either one ?
Forum: Bioinformatics 03-24-2010, 11:15 AM
Replies: 2
Views: 2,788
Posted By sowmyai
I too noticed that all most of my SNPs had...

I too noticed that all most of my SNPs had quality score of 228. But I had a couple of 255s. Did you ever find out what's magical about 228 ?
Forum: Bioinformatics 03-22-2010, 09:21 AM
Replies: 0
Views: 2,621
Posted By sowmyai
SAMtools - p-value for SNP quality

Could someone please tell me how the p-value is calculated and fed into the PHRED score (which is just a log function of the p-value as I understand it) in SAMtools ?
Forum: Bioinformatics 03-20-2010, 10:22 PM
Replies: 2
Views: 1,938
Posted By sowmyai
One more question. Are Solexa paired-end read...

One more question. Are Solexa paired-end read mates from the same or opposite strands ?
Forum: Bioinformatics 03-20-2010, 10:20 PM
Replies: 2
Views: 1,938
Posted By sowmyai
Sequencing ssRNA virus using Bowtie

I am trying to assemble reads from an ssRNA virus into a reference genome. In this case, does strand bias apply ? Also, how should the second column of the Bowtie output "Reference strand(+/-) of the...
Forum: Bioinformatics 02-11-2010, 12:38 PM
Replies: 1
Views: 2,542
Posted By sowmyai
AMOScmp

I am trying to run AMOScmp with 6 reference genomes. I don't get an error in the log files but I get a zero-size contig file.

Any clues why ?
Showing results 1 to 25 of 27

 


All times are GMT -8. The time now is 05:10 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO