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Search: Posts Made By: kwicher
Forum: Bioinformatics 09-07-2011, 09:04 AM
Replies: 5
Views: 3,778
Posted By kwicher
I somehow made it: I made a bash script which...

I somehow made it:
I made a bash script which first export the PATH with directories to tophat,bowtie, and samtools; and then runs the tophat.

I am running this script from within qsub with...
Forum: Bioinformatics 09-07-2011, 06:12 AM
Replies: 5
Views: 3,778
Posted By kwicher
Thanks but it does not unfortunately; I run ...

Thanks but it does not unfortunately; I run

qsub -b y -e /mnt/fastfs/KW_Temp/installs -o /mnt/fastfs/KW_Temp/installs/ "echo $PATH > bow"

I have put PATH to both .bashrc and .profile files but...
Forum: Bioinformatics 09-07-2011, 04:09 AM
Replies: 5
Views: 3,778
Posted By kwicher
Tophat cannot evoke bowtie from under qsub

Hi

I come across a strange problem. I have all the latest tophat, bowtie, samtools installed locally. All the tree programs are also in my $PATH.

When I run tophat on the test sequences it does...
Forum: Bioinformatics 09-04-2011, 04:13 AM
Replies: 21
Views: 5,428
Posted By kwicher
Thanks. Here is how I converted the reference...

Thanks.
Here is how I converted the reference genome, indexed it and tried to make the alignment.
- converting genome
/mnt/fastfs/bin/bfast fasta2brg -A 1 -f refseq.fas

- INDEXING
qsub -q...
Forum: Bioinformatics 09-03-2011, 05:53 PM
Replies: 21
Views: 5,428
Posted By kwicher
More details

Thank you.

I run the bfast match with -s 1 and -e 1 (the same is for -e 100) and the full error message is:
************************************************************
Checking input parameters...
Forum: Bioinformatics 09-03-2011, 04:41 PM
Replies: 21
Views: 5,428
Posted By kwicher
Bfast memory corruption error on all 8 read files

Hello

I have 8 files with 50bp SE SOLiD reads. For each and single file I am getting the same error during match step:
*** glibc detected *** /mnt/fastfs/bin/bfast: malloc(): memory corruption:...
Forum: SOLiD 09-01-2011, 11:07 AM
Replies: 1
Views: 3,522
Posted By kwicher
BWA parameters for mRNA-seq aligning against mRNA refseq

Hello

I am sure similar questions were posted earlier but I could not find the definitive answer.

So the question is what parameeters would you use for mapping 1/16 chip data from single-cell...
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