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Forum: Bioinformatics 12-12-2012, 03:47 AM
Replies: 3
Views: 2,743
Posted By mixter
Hello Felix, Thanks for the detailed...

Hello Felix,

Thanks for the detailed explanation, so, that means that it's conceptually possible but with the caveats you mentioned.

Meanwhile I'm practically interested in doing this, i.e....
Forum: Bioinformatics 11-28-2012, 05:06 AM
Replies: 3
Views: 2,743
Posted By mixter
Bismark and unique matches

Hello,

I have a mostly theoretical question which my group would need to adress, though. Bismark (and possibly, other methylation mappers) have a hardcoded behavior of allowing only the unique...
Forum: Bioinformatics 11-26-2012, 05:29 AM
Replies: 1
Views: 1,219
Posted By mixter
Accessing SAM CIGAR strings in ShortRead (Bioconductor)

Hi,

I am looking for a function or accessor in the R/Bioconductor package ShortRead, or something that uses the same standard format, that is able to get me the CIGAR strings.

I'm commonly...
Forum: Epigenetics 10-10-2012, 03:41 AM
Replies: 5
Views: 2,358
Posted By mixter
Hello, Many thanks for the help. I've tried...

Hello,

Many thanks for the help. I've tried making these modifications, but it seems I need a bit more help. The mismatch number was not displayed in SAM output for either- single or paired-end...
Forum: Epigenetics 10-01-2012, 05:26 AM
Replies: 5
Views: 2,358
Posted By mixter
Non-BS mismatch count in .SAM (esp. Bismark)?

Hello,

This question should be of general interest, and judging from documentation/publication I am not sure about the issue, so here it goes:

In Bismark, where can I see the number of...
Forum: RNA Sequencing 07-09-2012, 06:28 AM
Replies: 2
Views: 2,262
Posted By mixter
Addendum: This seems to be a non-issue. I found...

Addendum: This seems to be a non-issue. I found that the GTF file in question was actually corrupted.

Nicer error reporting to spot errors from tophat's utilities would be appreciated in future...
Forum: RNA Sequencing 07-09-2012, 05:40 AM
Replies: 2
Views: 2,262
Posted By mixter
Tophat 2.0.4 and GTF conversion failure -- bug?

Hello,

I'm experiencing the following problem with tophat2 and haven't seen it described before nor able to debug it yet. I hope someone can make suggestions. Note that I can use my tophat...
Forum: Epigenetics 06-08-2012, 03:07 AM
Replies: 3
Views: 3,439
Posted By mixter
Dear Simon, What you wrote here made a lot...

Dear Simon,

What you wrote here made a lot of sense and I have meanwhile adopted this practice of not filtering reads to correct for conversion rate. There are several options I'm exploring,...
Forum: Bioinformatics 04-11-2012, 12:33 AM
Replies: 1
Views: 966
Posted By mixter
Hi, There's a verbose description of each...

Hi,

There's a verbose description of each column under http://cufflinks.cbcb.umd.edu/manual.html#cuffcomp_output

Also, in my experience, for a lot of technical questions and concerns the FAQ is...
Forum: Epigenetics 04-06-2012, 11:13 AM
Replies: 4
Views: 5,510
Posted By mixter
Thanks, even though I'm having these issues with...

Thanks, even though I'm having these issues with single-end sample, the paired-end information is valuable.

I have a rather strange case where a medium-quality sequencing run is yielding almost...
Forum: Epigenetics 04-05-2012, 09:25 AM
Replies: 4
Views: 5,510
Posted By mixter
Methylation calling tools, what works well?

Hi all,

I'm looking for a stable standalone tool to call methylation from mapped reads, in my case from RRBS. I also need to be able to call non-CpG methylation in some way.

[Reason: I'm...
Forum: Epigenetics 03-05-2012, 03:56 AM
Replies: 2
Views: 3,625
Posted By mixter
Many thanks! For now, we are just looking at...

Many thanks! For now, we are just looking at public data sets. I just wanted to say that we found this an extremely helpful orientation.
Forum: Epigenetics 02-28-2012, 07:48 AM
Replies: 2
Views: 3,625
Posted By mixter
BS-Seq mapping efficiency, what can be expected?

Hi,

I'm interested in references to expected and acceptable mapping efficiency (i.e. % of mappable reads) in different BS-Seq scenarios due to my own experiments but this should also be of general...
Forum: Epigenetics 02-13-2012, 03:17 PM
Replies: 3
Views: 3,439
Posted By mixter
Bisulfite sequencing - filtering by min. conversion rate

Hi,

I am looking into filtering bisulfite reads by a minimum conversion rate. Something high like a 95% CpG and non-CpG conversion rate. I've been working with Bismark and really like it.

I...
Forum: Epigenetics 01-19-2012, 03:56 AM
Replies: 1
Views: 3,061
Posted By mixter
Bismark paired-end positions

Hello,

I noticed that Bismark paired-end runs give you an output with start/stop genomic positions only for the first read, but not for its mate.

As the two mates overlap but do not have...
Forum: Epigenetics 06-28-2011, 01:52 AM
Replies: 0
Views: 1,431
Posted By mixter
Smile Fasta with one entry per chromosome (for methylation analysis and others)

Hello,

I'm currently evaluating different tools for methylation analysis of HTS data (bisulfite, RRBS). I already know and use Bismark, but I'd prefer to also handle data directly in...
Forum: Genomic Resequencing 05-30-2011, 03:51 AM
Replies: 5
Views: 18,852
Posted By mixter
Hi, I have run into the same problem,...

Hi,

I have run into the same problem, however, your solution of removing the -v option in the samtools pileup call did not work for me. I still get sequences consisting of long stretches of...
Forum: Bioinformatics 05-22-2011, 03:00 AM
Replies: 14
Views: 30,129
Posted By mixter
Question Consensus FASTA from BAM files

Hi,

I'm currently trying to get a consensus sequence that is specific to individual humans, from the 1000 genomes project data available in BAM format at...
Forum: Bioinformatics 10-18-2010, 12:01 AM
Replies: 1
Views: 1,934
Posted By mixter
Question Retrieving single bases of the reference genome in R

Hello,

Given a chromsome and single-base position for a species, I need to retrieve the called base in the reference genome. I'm looking for an existing way with R/Bioconductor for this.

I am...
Forum: Bioinformatics 09-13-2010, 01:36 AM
Replies: 3
Views: 4,937
Posted By mixter
Allele counts from MAQ snp output

Hello,

I have an additional question, after having read this thread and the documentation.

What I need would be the direct counts for the reference and variant allele, like in VarScan, for...
Forum: Bioinformatics 07-03-2010, 05:03 AM
Replies: 2
Views: 5,517
Posted By mixter
"R Killed" when working with large BAM files

I'm trying to work with large BAM files produced by bowtie alignment of illumina sequencing runs. I'm able to work with them fine with tools outside of R, but R seems to have some limitations or...
Forum: Bioinformatics 06-11-2010, 02:11 AM
Replies: 2
Views: 5,099
Posted By mixter
Bump. I'm also a bit confused by this message, in...

Bump. I'm also a bit confused by this message, in my case it reports merging 6 files. I use 3 lanes labeled with 5 barcodes each. To be sure I put each barcode-specific alignment in a separate...
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