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Forum: Bioinformatics 07-22-2014, 04:53 AM
Replies: 3
Views: 4,406
Posted By SquirrelSeq
Hello Brian, thank you for the answer. ...

Hello Brian,

thank you for the answer.

The whole confusion is caused by the mix-up of two different definitions of "plus"/"+" and "minus"/"-", when people are talking about single genes on the...
Forum: Bioinformatics 07-21-2014, 05:12 AM
Replies: 3
Views: 4,406
Posted By SquirrelSeq
Strand specificity of genome fasta files (hg19)

Hello everybody,

do genomic reference FASTA files, such as famous hg19.fa,
usually contain
one continuous physical strand, meaning that sense (plus) and antisense (minus) sections are shown in...
Forum: Bioinformatics 06-12-2013, 05:20 AM
Replies: 6
Views: 3,131
Posted By SquirrelSeq
That is an idea. But as far as I know, I could...

That is an idea. But as far as I know, I could only see enriched sequences. Is this really enough, to identify primers/adapters? Also other sequences could be enriched, especially in specific...
Forum: Bioinformatics 06-12-2013, 05:02 AM
Replies: 6
Views: 3,131
Posted By SquirrelSeq
I downloaded several promising libraries. ...

I downloaded several promising libraries.

Some of them are documented not very detailedly. Before mapping, I normally trim adapters and primers. Are these already trimmed in the public data...
Forum: Bioinformatics 06-07-2013, 06:48 AM
Replies: 3
Views: 2,886
Posted By SquirrelSeq
Where can I get reference genomes and transcriptomes of E.coli and S. cerevisiae?

Hello everybody,

does anyone know, where I could download reference genomes and/or transcriptomes of E.coli and S.cerevisiae?

Best regards,
SquirrelSeq
Forum: Bioinformatics 06-07-2013, 06:45 AM
Replies: 6
Views: 3,131
Posted By SquirrelSeq
Thank you for your help, that was highly useful!

Thank you for your help, that was highly useful!
Forum: Bioinformatics 06-06-2013, 07:14 AM
Replies: 6
Views: 3,131
Posted By SquirrelSeq
total RNA/transcriptome of E.coli or S.cerevisiae

Hello everybody,

I'm looking for a repository/archive/database, where I can download FASTQ files of NGS Deep Sequencing runs of E.coli and S.cerevisiae.

Can anybody tell me, where I can find...
Forum: Bioinformatics 05-23-2013, 02:10 AM
Replies: 0
Views: 644
Posted By SquirrelSeq
Pileup: Only reads reaching the 3'end

Hello everybody,

I have pileup files with multiple short references that are covered by reads. I want to keep only the coverage information of reads reaching the 3'ends of these references. (That...
Forum: Bioinformatics 05-17-2013, 06:48 AM
Replies: 2
Views: 1,336
Posted By SquirrelSeq
I know that Samtools is very common in NGS data...

I know that Samtools is very common in NGS data analysis.

So is my question confusing or not precise enough?
Forum: Bioinformatics 05-13-2013, 02:51 AM
Replies: 2
Views: 1,336
Posted By SquirrelSeq
Show uncovered positions in pileup files

Hello everyone,

I created pileup files from sam/bam files via Samtools.

For every reference in the alignment, the pileup entries start from the 5'-most reference position that is covered by...
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