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Forum: Bioinformatics 03-23-2015, 04:07 AM
Replies: 0
Views: 779
Posted By hrseq
Pipeline for analysis sgRNA negative selection screens

Hi

Is there a pipeline or recommended procedure for analyzing read data coming from sgRNA screens for negative selection?

Best regards
Hubert
Forum: Genomic Resequencing 12-05-2013, 09:32 AM
Replies: 6
Views: 3,085
Posted By hrseq
finding deletions of length 20 - 50bp from 100bp reads

Hi

What would be the suggested approach to find deletions in the range of 20 - 50 bp in human data? The reads are 100bp illumina reads.

Any suggestions?

regards
hubet
Forum: Bioinformatics 11-05-2013, 06:21 AM
Replies: 3
Views: 1,754
Posted By hrseq
Thanks, I know those, but with what should I feed...

Thanks, I know those, but with what should I feed them?

The unique or all sequences from unigene??
Forum: Bioinformatics 11-05-2013, 05:37 AM
Replies: 3
Views: 1,754
Posted By hrseq
RNA-seq with UniGene sequences as target

Hi all

What is the best approach when I want to get expression estimates from RNA-seq data for a species where the full genome does not exist but UniGene has a lot of sequences for it? In my case...
Forum: Bioinformatics 09-13-2013, 05:56 AM
Replies: 0
Views: 1,516
Posted By hrseq
bwa-mem artifact with deletions

Hi

when I run bwa-mem with the options "-w 100 -O 5 -E 0.4" on paired end data I get the distribution of deletion sizes as shown in the attached image.

Can anybody give a hint where this spiky...
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