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Search: Posts Made By: kostask
Forum: Bioinformatics 01-31-2016, 09:55 AM
Replies: 2
Views: 1,200
Posted By kostask
Thank you westerman I saw exactly the flags...

Thank you westerman

I saw exactly the flags and the corresponding reads for each one.

Wouid it be correct if I wanted to extract reads with certain flags (specifically 67, 131, 115 and 179) to...
Forum: Bioinformatics 01-26-2016, 03:02 PM
Replies: 2
Views: 1,200
Posted By kostask
extract_only_concordant_paired_reads_from_bam_file

Hi everyone,

I am trying to extract only concordant paired reads from my bam file using a command that I found in posts with similar subject:

https://www.biostars.org/p/95929/
...
Forum: Bioinformatics 01-22-2016, 12:51 PM
Replies: 3
Views: 1,301
Posted By kostask
Thank you GenoMax, I will be sure to check out...

Thank you GenoMax, I will be sure to check out BBMap.



So your opinion is that the presence of at least some of these kmers in illumina adapters is random? Or that it will pose no problem?
Forum: Bioinformatics 01-22-2016, 05:06 AM
Replies: 3
Views: 1,301
Posted By kostask
Adapter_and_kmer_trimming

Hi everyone,

I am using publicly available, 51 bp paired-end RNA seq data and I have some questions concerning the quality trimming of the data before passing them to Tophat2 for mapping.
...
Forum: Bioinformatics 10-01-2015, 02:16 PM
Replies: 3
Views: 988
Posted By kostask
Actually I used RNA-seq data and I performed the...

Actually I used RNA-seq data and I performed the SNP calling step on human genome version hg19.

No it returns both + and - strand since it usually contains reads corresponding to both orientations.
Forum: Bioinformatics 09-24-2015, 06:29 AM
Replies: 3
Views: 988
Posted By kostask
Strand info, SNPs

Hello,

I am performing an analysis for SNPs in Galaxy UCSC, using the tools mpileup (to generate pileup from bam files) and Varscan (to generate vcf from pileup files).

Although the programs...
Forum: Bioinformatics 09-11-2015, 02:55 AM
Replies: 2
Views: 1,140
Posted By kostask
Thanks jesus garcia, it works fine now!

Thanks jesus garcia, it works fine now!
Forum: Bioinformatics 09-09-2015, 08:15 AM
Replies: 2
Views: 1,140
Posted By kostask
Annovar no such file or directory

Hi everyone,

I'm new to Annovar so I tried to follow the Quick Start-Up Guide for table_annovar program.

Specifically I downloaded hg19 refGene database (perl annotate_variation.pl -buildver...
Showing results 1 to 8 of 8

 


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