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Forum: Bioinformatics 02-07-2014, 01:23 AM
Replies: 5
Views: 1,458
Posted By ChrisAU
Maybe also try running "fastqc -k 10 ..." to...

Maybe also try running "fastqc -k 10 ..." to increase the kmer-size fastqc is looking for. That way, you get a better picture of what sequence is at the end of your reads. You most probably have to...
Forum: Bioinformatics 02-07-2014, 01:16 AM
Replies: 9
Views: 4,355
Posted By ChrisAU
I've also had good experience with Blast2GO, it...

I've also had good experience with Blast2GO, it doesn't require installation and is quite easy to handle. Also, they updated the quite ugly colours of their pie charts ;)
Forum: Bioinformatics 07-26-2013, 05:45 AM
Replies: 2
Views: 1,171
Posted By ChrisAU
Hi Raff, I performed ALLPATHS-LG assemblies...

Hi Raff,

I performed ALLPATHS-LG assemblies with only a 2kb or 4kb mate-pair library (additional to the paired-end library of course) without any problem or obvious drop in the assembly quality.
...
Forum: Bioinformatics 11-16-2012, 05:26 AM
Replies: 1
Views: 4,108
Posted By ChrisAU
bowtie chunkmbs - Exhausted best-first chunk memory

Hi,

perhaps somebody can solve this little mystery for me.

Running bowtie --chunkmbs 512 worked without any errors/warnings.
As the mapping statistic was not as I expected, among other things,...
Forum: Bioinformatics 09-13-2012, 11:51 PM
Replies: 2
Views: 1,913
Posted By ChrisAU
It worked fine for paired-end reads, but not for...

It worked fine for paired-end reads, but not for the mate pairs.
Reverse complementing the first read should do the trick though. For the quality string, I just replaced the default quality string...
Forum: Bioinformatics 09-11-2012, 07:05 AM
Replies: 2
Views: 1,913
Posted By ChrisAU
dwgsim illumina mate pairs

Hi there,

I want to simulate Illumina mate pairs and thought of using dwgsim.
However, the manual states that it will create mate pairs, that have --> --> orientation, whereas Illumina mate pairs...
Forum: Bioinformatics 02-26-2012, 11:49 AM
Replies: 3
Views: 1,342
Posted By ChrisAU
I have two gene models from Cufflinks and a third...

I have two gene models from Cufflinks and a third one. They are quite similar for the most part, however, in some regions the exon-intron structure differs. The objective is, to calculate the most...
Forum: Bioinformatics 02-24-2012, 04:20 AM
Replies: 3
Views: 1,342
Posted By ChrisAU
Consensus gene model

Hi all,

I have three different transcript annotations in gff format, two of them were generated by Cufflinks. Now I would like to build a consensus gene model out of the three. Do you have any...
Forum: RNA Sequencing 01-23-2012, 03:59 AM
Replies: 0
Views: 2,053
Posted By ChrisAU
GSNAP Output splice junctions

Matter resolved, thread can be closed.
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