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Search: Posts Made By: Derek-C
Forum: Bioinformatics 02-22-2013, 02:52 AM
Replies: 9
Views: 13,124
Posted By Derek-C
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...
Forum: Bioinformatics 01-21-2013, 01:18 AM
Replies: 0
Views: 678
Posted By Derek-C
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...
Forum: Bioinformatics 01-14-2013, 06:01 AM
Replies: 2
Views: 1,411
Posted By Derek-C
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...
Forum: Bioinformatics 01-14-2013, 03:31 AM
Replies: 2
Views: 1,411
Posted By Derek-C
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...
Forum: Bioinformatics 11-13-2012, 02:30 AM
Replies: 3
Views: 2,339
Posted By Derek-C
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?
Forum: Bioinformatics 11-13-2012, 02:15 AM
Replies: 0
Views: 1,166
Posted By Derek-C
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...
Forum: Bioinformatics 11-12-2012, 01:05 AM
Replies: 3
Views: 2,339
Posted By Derek-C
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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