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Search: Posts Made By: muol
Forum: Bioinformatics 07-03-2014, 01:59 PM
Replies: 22
Views: 5,268
Posted By muol
Thanks, the phiX filtering step worked well. It...

Thanks,
the phiX filtering step worked well. It reported 5% phiX content, which is pretty close to our requested 4% spike for this run.

The second step mapped 99.7% of the filtered reads to 16S,...
Forum: Bioinformatics 07-03-2014, 01:05 PM
Replies: 22
Views: 5,268
Posted By muol
Hi Brian, Would you recommend to use BBDuk...

Hi Brian,

Would you recommend to use BBDuk for pre-filtering reads from microbiome samples? I thought about cleaning out phiX contaminants as described above, followed by extracting 16S rDNA reads...
Forum: Bioinformatics 06-27-2014, 05:11 PM
Replies: 24
Views: 7,742
Posted By muol
Excellent, just did a test run. This is very...

Excellent, just did a test run. This is very useful software!

Olaf
Forum: Bioinformatics 06-23-2014, 08:14 PM
Replies: 24
Views: 7,742
Posted By muol
Thanks for the info Brian, it wasn't a big issue....

Thanks for the info Brian, it wasn't a big issue.

Olaf
Forum: Bioinformatics 06-23-2014, 06:07 PM
Replies: 24
Views: 7,742
Posted By muol
Brian, I ran into a smaller issue with...

Brian,

I ran into a smaller issue with bbnorm. When trying to input and output separate files for a PE library like this:

bbnorm.sh in1=R1.fastq.gz in2=R2.fastq.gz out1=R1.bbnorm.fastq.gz...
Forum: Bioinformatics 06-23-2014, 04:54 PM
Replies: 24
Views: 7,742
Posted By muol
Indeed, just tried it and it works well with...

Indeed, just tried it and it works well with bbnorm.

Thanks
Olaf
Forum: Bioinformatics 06-23-2014, 04:28 PM
Replies: 24
Views: 7,742
Posted By muol
Hi Brian, Is there an option to set read...

Hi Brian,

Is there an option to set read quality encoding in bbnorm? I had to set qin=33 in bbduk for some Illumina 1.9 paired end libraries, but this option doesn't seem to exist in bbnorm (used...
Forum: Bioinformatics 07-04-2013, 08:37 AM
Replies: 3
Views: 1,846
Posted By muol
Velvet ignores fastq headers and replaces them...

Velvet ignores fastq headers and replaces them with its own (fasta) headers anyway. You just have to make sure that input read pairs are either shuffled in one file, or synced if separate files are...
Forum: Bioinformatics 07-04-2013, 08:19 AM
Replies: 6
Views: 1,572
Posted By muol
Abacas' blind spot is show-tiling from mummer,...

Abacas' blind spot is show-tiling from mummer, and I guess your nucmer.tiling file is empty, causing this Perl error. It happens if show-tiling cannot stitch together the consensus from nucmer.delta....
Forum: Bioinformatics 06-18-2012, 02:27 PM
Replies: 13
Views: 5,026
Posted By muol
Hello, I get a very similar error in...

Hello,

I get a very similar error in htseq-count (ubuntu 10.10 x64, Python 2.6.6, HTseq-0.5.3p7):

htseq-count -mintersection-nonempty -s no -t mRNA -i ID accepted_hits.sam...
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