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Forum: Bioinformatics 11-30-2016, 03:05 PM
Replies: 3
Views: 1,352
Posted By runnerBio88
Thanks I did some test and as you said that...

Thanks

I did some test and as you said that is what vcf-merge does.

I've alse checked bcftools merge, but as the input paramters are almost the same I used vcf-merge.

Is it worthy to use...
Forum: Bioinformatics 11-30-2016, 03:03 AM
Replies: 3
Views: 1,352
Posted By runnerBio88
vcf-merge

Hi

I have several vcf files, raw and annotated.
I've used vcf-merge without any option. The output file I used it check for recurrent mutations.

I'm not able to understand (as the...
Forum: Bioinformatics 01-14-2016, 02:55 AM
Replies: 3
Views: 2,734
Posted By runnerBio88
Thanks I'll give a try to BBMerge to calculate...

Thanks I'll give a try to BBMerge to calculate insert size, as I'm not sure that using Bowtie2 to calculate this is a good option.

Thanks
Forum: Bioinformatics 01-13-2016, 06:29 AM
Replies: 3
Views: 2,734
Posted By runnerBio88
SAM output from bowtie2

Hi

I have some data from RNAseq which I'm going to map using tophat, but because I don't know the inner mate distance I'm mapping using bowtie2 to get to know this inner distance between reads (I...
Forum: RNA Sequencing 12-29-2015, 06:20 AM
Replies: 3
Views: 1,527
Posted By runnerBio88
RNA-seq for Variant calling

Hi

I've read a few number of papers about this topic such:
http://www.sciencedirect.com/science/article/pii/S0002929713003832...
Forum: Bioinformatics 12-11-2015, 01:05 AM
Replies: 1
Views: 1,122
Posted By runnerBio88
Well, I have seen that most of my doubts are...

Well, I have seen that most of my doubts are explained not in the manual but in the paper.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007767
Forum: Bioinformatics 12-11-2015, 12:34 AM
Replies: 1
Views: 1,122
Posted By runnerBio88
Indexing with bfast

Hi

I'm starting to use bfast and I have some doubts about some indexing parameters.

When indexing do I have to do it with the 10 spaced seed? I know this is to create different indexes to find...
Forum: Bioinformatics 10-31-2015, 04:08 PM
Replies: 2
Views: 981
Posted By runnerBio88
Well, I just found a nice explanation right after...

Well, I just found a nice explanation right after I posted this, sorry!

http://www.homolog.us/Tutorials/index.php?p=3.1&s=2
Forum: Site Feedback/Suggestions 10-31-2015, 04:01 PM
Replies: 11
Views: 9,059
Posted By runnerBio88
I posted something, then I found the answer in...

I posted something, then I found the answer in the web. Should be able to delete my post.
Forum: Bioinformatics 10-31-2015, 03:49 PM
Replies: 2
Views: 981
Posted By runnerBio88
Kmer frequency

Hi

I'm new in this and I'm trying to understand the output of SOAPdenovo, in particular the file *.kmerFreq. I've tried to find how to interpret it in the web, but after some time I have no clue...
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