Forum: Bioinformatics
02-22-2013, 03:52 AM
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Replies: 9
Views: 15,141
Sorry to bump an old question, but I'm also...
Sorry to bump an old question, but I'm also wondering about this at the moment and I can't seem to find an answer anywhere.
What are the merits of using the human transcriptome vs human genome...
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Forum: Bioinformatics
01-21-2013, 02:18 AM
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Replies: 0
Views: 788
removing singletons from tophat output
Hi all,
I'm trying to get my tophat output without singletons (I'm trying to convert the output back into fastq format so everything needs a mate) but even with both the no-mixed and...
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Forum: Bioinformatics
01-14-2013, 07:01 AM
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Replies: 2
Views: 1,609
Are you certain about the singletons thing? It...
Are you certain about the singletons thing? It would make sense, butl I just did some checking there with samtools flagstat and according to the numbers I'm looking at for this one accepted_hits.bam...
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Forum: Bioinformatics
01-14-2013, 04:31 AM
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Replies: 2
Views: 1,609
bam2fastq discarded reads
Hi all,
I've been using bam2fastq on my tophat output and it's been great, runs really quickly, except for the number of reads being discarded. For example this was for one of my output files from...
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Forum: Bioinformatics
11-13-2012, 03:30 AM
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Replies: 3
Views: 2,699
Yup thats right.
I'm sorry I'm not quite...
Yup thats right.
I'm sorry I'm not quite understanding what you mean? If reads that fail to map are included in another file, then how is it that only 30% of the reads in the other file mapped?
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Forum: Bioinformatics
11-13-2012, 03:15 AM
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Replies: 0
Views: 1,422
Ribozero Output
Hi all,
I have some rRNA which was filtered out of my total RNA sample using Ribopicker. My sequence data is paired ends. I was wondering if it was possible to have Ribopicker output the actual...
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Forum: Bioinformatics
11-12-2012, 02:05 AM
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Replies: 3
Views: 2,699
Bowtie2 Sam output
Hey guys,
I'm somewhat new to bioinformatics and I'm using bowtie2 with transcriptomic data, but there's something I don't quite understand. I'm mapping my transcripts to a version of the NCBI...
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