Forum: Bioinformatics
02-09-2017, 10:14 AM
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Replies: 18
Views: 15,768
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Forum: Bioinformatics
05-05-2014, 06:01 PM
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Replies: 1
Views: 1,626
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...
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Forum: Bioinformatics
04-18-2014, 09:13 AM
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Replies: 8
Views: 2,429
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...
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Forum: Bioinformatics
04-18-2014, 08:39 AM
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Replies: 8
Views: 2,429
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Forum: Bioinformatics
04-13-2014, 02:40 PM
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Replies: 3
Views: 1,059
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Forum: Bioinformatics
07-16-2010, 09:42 AM
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Replies: 366
Views: 204,500
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Forum: Bioinformatics
07-16-2010, 09:10 AM
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Replies: 366
Views: 204,500
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Forum: Bioinformatics
07-16-2010, 08:54 AM
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Replies: 366
Views: 204,500
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...
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Forum: Bioinformatics
07-16-2010, 08:42 AM
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Replies: 366
Views: 204,500
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Forum: Bioinformatics
07-16-2010, 08:10 AM
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Replies: 366
Views: 204,500
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Forum: Bioinformatics
07-16-2010, 08:06 AM
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Replies: 366
Views: 204,500
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...
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Forum: Bioinformatics
07-16-2010, 07:21 AM
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Replies: 2
Views: 3,232
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Forum: Bioinformatics
07-15-2010, 07:13 AM
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Replies: 14
Views: 8,109
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Forum: Bioinformatics
07-14-2010, 07:09 AM
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Replies: 2
Views: 7,051
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Forum: Bioinformatics
07-13-2010, 08:22 AM
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Replies: 2
Views: 7,051
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...
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Forum: Bioinformatics
07-11-2010, 06:38 PM
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Replies: 5
Views: 4,142
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Forum: Bioinformatics
07-07-2010, 08:10 AM
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Replies: 5
Views: 4,142
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...
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Forum: Bioinformatics
07-06-2010, 12:23 PM
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Replies: 5
Views: 4,142
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 ?...
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Forum: Bioinformatics
04-30-2010, 10:12 AM
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Replies: 4
Views: 2,543
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Forum: Bioinformatics
03-24-2010, 11:29 AM
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Replies: 0
Views: 1,266
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 ?
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Forum: Bioinformatics
03-24-2010, 11:15 AM
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Replies: 2
Views: 2,788
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Forum: Bioinformatics
03-22-2010, 09:21 AM
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Replies: 0
Views: 2,621
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 ?
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Forum: Bioinformatics
03-20-2010, 10:22 PM
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Replies: 2
Views: 1,938
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Forum: Bioinformatics
03-20-2010, 10:20 PM
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Replies: 2
Views: 1,938
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...
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Forum: Bioinformatics
02-11-2010, 12:38 PM
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Replies: 1
Views: 2,542
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 ?
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