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Search: Posts Made By: hmortens
Forum: Bioinformatics 10-28-2013, 07:30 AM
Replies: 2
Views: 3,839
Posted By hmortens
Simon Andrews just wrote back to...

Simon Andrews just wrote back to clarify...hoorah!
Simple answer, but the manual is not clear on this point.
fastqc --casava *.fastq.gz

Running it now...
Forum: Bioinformatics 10-28-2013, 05:17 AM
Replies: 2
Views: 3,839
Posted By hmortens
FASTQC setting for multiple casava fastq files?

I am using fastqc in my workflow, but am wondering how to get the program to recognize multiple cassava fastq files, as described in the manual.
My command for a single fastq is like:
/fastqc...
Forum: Bioinformatics 07-10-2013, 04:45 AM
Replies: 6
Views: 3,788
Posted By hmortens
thanks kennels and visserm. I actually got an...

thanks kennels and visserm. I actually got an update for miRbase 19 from the miRanalyzer folks, so it seems they are pretty on top of it.
Marike, regarding the bowtie indexing...Can you describe...
Forum: Bioinformatics 07-09-2013, 12:59 PM
Replies: 1
Views: 989
Posted By hmortens
you can use miRanalyzer. but i am not sure how to...

you can use miRanalyzer. but i am not sure how to update to the current miRbase version.
have you had any success otherwise?
Forum: Bioinformatics 07-09-2013, 11:30 AM
Replies: 3
Views: 1,715
Posted By hmortens
it was a pain to install. but I got it working....

it was a pain to install. but I got it working. now i wonder if the miRbase versions that the DB is built with are really old?
Forum: Bioinformatics 07-09-2013, 11:29 AM
Replies: 6
Views: 3,788
Posted By hmortens
miRNA analysis with bowtie, miRanalyzer or other

I have just tested miRanalyzer and am now realizing that it may not use a very recent version of miRbase. The database construction is not trivial for this program however, and the bowtie indexes for...
Forum: Bioinformatics 08-23-2012, 08:03 AM
Replies: 15
Views: 10,227
Posted By hmortens
How did you re-build the index without the random...

How did you re-build the index without the random chromosomes????
Forum: Bioinformatics 07-30-2012, 07:24 AM
Replies: 0
Views: 1,345
Posted By hmortens
BIG difference in number of genes mapped with tophat vs. casava 1.8.2

Having run casava and tophat on the same libraries we found that the tophat output has about 40% more mapped reads than did the casava output.
Looking across genes, we furthermore found that...
Forum: Bioinformatics 01-09-2012, 10:26 AM
Replies: 2
Views: 2,615
Posted By hmortens
I am using Joe Pickrell's data...

I am using Joe Pickrell's data (http://eqtl.uchicago.edu/RNA_Seq_data/), which I believe are single end reads, and have been running them as such using the following settings.

> time tophat -r 200...
Forum: Bioinformatics 01-09-2012, 09:58 AM
Replies: 2
Views: 2,615
Posted By hmortens
tophat/Cufflinks workflow question

I am still trying to make sure that I am running tophat/cufflinks in the most effective way, and was hoping folks might pass on how they set up their workflows.
I am testing four fastq files...
Forum: Bioinformatics 11-17-2011, 05:30 AM
Replies: 1
Views: 1,446
Posted By hmortens
modifying bowtie settings from tophat

*Hi,
I am attempting to modify the default settings that Tophat specifies for Bowtie to improve alignments.
I have tried the -g, -k, and -m options from within tophat. I am not getting tophat to...
Forum: Bioinformatics 08-10-2011, 06:55 AM
Replies: 3
Views: 3,671
Posted By hmortens
sample Illumina RNAseq datasets

hi,
I am attempting to start a workflow setup for RNAseq analyses. I would like to get a hold of a reasonably sized Illumina RNAseq dataset to do some data transfer tests and tests some of the...
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