Forum: Bioinformatics
07-14-2015, 07:13 PM
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Replies: 4
Views: 2,541
Fantastic! Thanks so much, Richard Finney.
...
Fantastic! Thanks so much, Richard Finney.
As I understand this command, it's saying to filter out anything with a mapping quality (MAPQ) score that is less than one and output that as a bam...
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Forum: Bioinformatics
07-14-2015, 02:53 PM
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Replies: 4
Views: 2,541
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Forum: Bioinformatics
03-11-2015, 02:46 PM
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Replies: 6
Views: 11,787
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Forum: Bioinformatics
03-11-2015, 01:45 PM
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Replies: 6
Views: 11,787
Hi GenoMax,
Thanks very much for the...
Hi GenoMax,
Thanks very much for the suggestion. I followed the instructions and they seemed to work in that the little snippet of test code worked as it should:
...
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Forum: Bioinformatics
03-11-2015, 10:25 AM
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Replies: 6
Views: 11,787
What is a kart file?
In trying to download files from SRA, I was directed to use part of the sratoolkit called "prefetch". There I came across the term "kart file":
...
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Forum: Bioinformatics
01-08-2014, 10:44 AM
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Replies: 17
Views: 49,539
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Forum: Bioinformatics
10-01-2013, 12:19 PM
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Replies: 2
Views: 1,160
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Forum: Bioinformatics
10-01-2013, 11:47 AM
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Replies: 2
Views: 1,160
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Forum: Bioinformatics
09-23-2013, 12:03 PM
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Replies: 6
Views: 4,329
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Forum: Bioinformatics
09-20-2013, 01:44 PM
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Replies: 6
Views: 4,329
Hi kokonech,
Thanks for the suggestion. I...
Hi kokonech,
Thanks for the suggestion. I finally figured it out - there was a version of bedtools that had this as a known bug. I updated to the latest version and the problem went away.
I...
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Forum: Bioinformatics
09-19-2013, 12:25 PM
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Replies: 6
Views: 4,329
bedtools coverage is inaccurate
I am using bedtools to calculate coverage in an RNA-seq bam file. I get screwy readings when it encounters a gap where there are no reads. Rather than filling it in with zeros, it takes a value that...
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Forum: Bioinformatics
05-11-2013, 02:12 PM
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Replies: 9
Views: 12,959
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Forum: Bioinformatics
05-01-2013, 01:02 PM
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Replies: 1
Views: 826
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Forum: Bioinformatics
05-01-2013, 09:40 AM
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Replies: 1
Views: 826
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Forum: Bioinformatics
05-01-2013, 09:33 AM
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Replies: 0
Views: 726
sequencing the silenced X chromosome
Is it more difficult to sequence the silenced X chromosome than the active X chromosome? I would think that all the methylation could easily cause difficulties.
Thanks.
Eric
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Forum: Bioinformatics
03-18-2013, 12:31 PM
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Replies: 0
Views: 1,876
NCBI's decryption tool
I have downloaded some files from NCBI's "Short Read Archive" (SRA). They come in an encrypted format. (The files have the extension "sra.ncbi_enc".) Directions for using this are here:
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Forum: Bioinformatics
02-01-2013, 04:09 PM
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Replies: 3
Views: 2,217
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Forum: Bioinformatics
01-31-2013, 05:04 PM
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Replies: 3
Views: 2,217
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Forum: Bioinformatics
12-24-2012, 04:01 PM
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Replies: 4
Views: 2,422
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Forum: Bioinformatics
12-24-2012, 03:49 PM
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Replies: 4
Views: 2,422
Hi aaronh,
I'm afraid I don't know what the...
Hi aaronh,
I'm afraid I don't know what the tmp dir is. Googling around, it looks like it's a temporary directory used for 'scratch' space. How can I specify it?
Since posting this, I ended...
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Forum: Bioinformatics
12-24-2012, 12:51 PM
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Replies: 4
Views: 2,422
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Forum: Bioinformatics
12-19-2012, 08:03 PM
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Replies: 7
Views: 2,064
I found out what the problem is with the 4.3...
I found out what the problem is with the 4.3 billion POS column: There is a bug in the version of gsnap that I was using that can lead to this type of thing with circular chromosomes. (The chromosome...
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Forum: Bioinformatics
12-18-2012, 04:32 PM
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Replies: 7
Views: 2,064
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Forum: Bioinformatics
12-18-2012, 03:08 PM
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Replies: 7
Views: 2,064
To follow up on this: The 35M16S CIGAR tells me...
To follow up on this: The 35M16S CIGAR tells me that the read is indeed hanging off the end. (My understanding of hard clipping versus soft clipping is that in both instances, some bases don't match...
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Forum: Bioinformatics
12-18-2012, 02:12 PM
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Replies: 7
Views: 2,064
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