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Forum: Site Feedback/Suggestions 03-23-2010, 10:24 AM
Replies: 3
Views: 3,462
Posted By kch
Mobile version of SEQanswers?

Is this possible? Specifically, it would be great if an optimized version was available for browsing on the iPhone/iPod Touch.
Forum: Bioinformatics 03-23-2010, 06:32 AM
Replies: 18
Views: 7,755
Posted By kch
You could maybe look into the fastx_collapser...

You could maybe look into the fastx_collapser tool from this package: http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
But I don't think it will report any counts.

Perhaps you could try...
Forum: RNA Sequencing 12-21-2009, 04:54 AM
Replies: 1
Views: 3,149
Posted By kch
At the very bottom of the TopHat manual under the...

At the very bottom of the TopHat manual under the heading TopHat Output, links are provided to the specification of each output file.

HTH
Forum: Bioinformatics 12-14-2009, 08:14 AM
Replies: 22
Views: 8,537
Posted By kch
I am using TopHat version 1.0.12 and Bowtie...

I am using TopHat version 1.0.12 and Bowtie version 0.11.3 with the "--solexa1.3-quals" flag as well. Similarly, I'm not sure whether the output in my accepted_hits.sam file is reporting ASCII-33...
Forum: Bioinformatics 12-01-2009, 12:13 PM
Replies: 2
Views: 2,807
Posted By kch
I was able to resolve this issue by following the...

I was able to resolve this issue by following the second set of instructions from here: http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#How_to_convert_SAM_to_BAM.3F


Hope...
Forum: Illumina/Solexa 11-30-2009, 07:16 AM
Replies: 3
Views: 2,300
Posted By kch
Thanks for your comments, simonandrews!

Thanks for your comments, simonandrews!
Forum: Illumina/Solexa 11-27-2009, 07:47 PM
Replies: 3
Views: 2,300
Posted By kch
ELAND reporting more than 2 mismatches?

In our s_N_sorted.txt file, we are finding cases in which ELAND appears to be reporting more than 2 mismatches, which sounds not at all plausible, as far as I understand. For example, we are getting...
Forum: Illumina/Solexa 09-30-2009, 07:42 PM
Replies: 4
Views: 2,715
Posted By kch
I'm also wondering about how TopHat handles these...

I'm also wondering about how TopHat handles these smaller segments. If the segment spans across a splice junction, can Bowtie align this or is this information lost?

Update: just re-read the paper...
Forum: Bioinformatics 09-01-2009, 11:13 AM
Replies: 1
Views: 2,029
Posted By kch
Hi nat, This might answer your question:...

Hi nat,

This might answer your question: http://seqanswers.com/forums/showthread.php?t=2183

The chromosome field is referring to contigs instead of chromosomes, which the UCSC Browser doesn't...
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