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Forum: RNA Sequencing 01-21-2015, 03:32 PM
Replies: 2
Views: 1,936
Posted By joseph
cummeRbund csScatter() error

Hello
Can you please help me find out why I am getting this error? Thanks

cuff = readCufflinks()
> cuff
CuffSet instance with:
3 samples
14017 genes
32101 isoforms
19668 TSS
Forum: Bioinformatics 08-31-2012, 03:59 PM
Replies: 4
Views: 3,120
Posted By joseph
--score-min bowitie2

Hi
I am using bowtie2.0.0-beta7 in --local mode to align SE 50 bases reads; I would like to change the parameter --score-min (default in --local mode is G,20,8) to increase the alignment score. Any...
Forum: Bioinformatics 08-22-2012, 10:55 AM
Replies: 2
Views: 1,352
Posted By joseph
tagdust output is not fastq!

Hi
can you please help me with the output of tagdust? It doesn't look like the proper fastq format.
Thanks
Joseph Dhahbi

tagdust contaminants.fasta myfile.fastq -fdr 0.05 -o...
Forum: Bioinformatics 12-28-2011, 07:39 PM
Replies: 4
Views: 2,205
Posted By joseph
I changed (print if $l < 60) to (print if $l =...

I changed (print if $l < 60) to (print if $l = 30)
here is the link again
http://biostar.stackexchange.com/questions/12433/bam-extract-only-alignment-with-a-specific-length
Forum: Bioinformatics 12-28-2011, 07:32 PM
Replies: 4
Views: 2,205
Posted By joseph
thanks. It worked.

thanks. It worked.
Forum: Bioinformatics 12-27-2011, 04:23 PM
Replies: 4
Views: 2,205
Posted By joseph
subsetting a bam file with specific alingment length

Hi
I would like to extract a bam file with alignments length = 30.
I tried a script that I found on BioStar:
http://biostar.stackexchange.com/questions/12433/answer
samtools view -h in.bam |...
Forum: Bioinformatics 12-20-2011, 05:24 PM
Replies: 2
Views: 4,003
Posted By joseph
thank you for your help.

thank you for your help.
Forum: Bioinformatics 12-20-2011, 01:01 PM
Replies: 2
Views: 4,003
Posted By joseph
how to extract raw unaligned reads?

Hello

I used bowtie to map sequencing reads:

> bowtie ~/hg19 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam
End-to-end 2/3-mismatch full-index search: 01:00:21
# reads processed:...
Forum: Bioinformatics 12-03-2011, 08:21 AM
Replies: 19
Views: 5,668
Posted By joseph
Hi Ethan it worked fine for me far...

Hi Ethan
it worked fine for me

far --source myfile.fastq --target myoutput.fastq --format fastq --adapters adapters.fasta --nr-threads 4

far --source SRR309288.fastq --target...
Forum: Bioinformatics 12-02-2011, 01:56 PM
Replies: 19
Views: 5,668
Posted By joseph
It works. Thank you.

It works. Thank you.
Forum: Bioinformatics 11-28-2011, 09:31 AM
Replies: 19
Views: 5,668
Posted By joseph
yes, please send me a precompiled binary. ...

yes, please send me a precompiled binary.
Thank you.
Joseph
Forum: Bioinformatics 11-27-2011, 12:45 PM
Replies: 19
Views: 5,668
Posted By joseph
these are the instructions from Readme.txt: ...

these are the instructions from Readme.txt:
MacOSX: Copy the libtbb.dylib from ./lib into your lib searchpath.

I copied ibtbb.dylib to /usr/local/bin
but I am not able to figure out from the...
Forum: Bioinformatics 11-27-2011, 10:41 AM
Replies: 19
Views: 5,668
Posted By joseph
help to install 'FAR - The Flexible Adapter Remover' on Mac OS

can you please show me how to install FAR on Mac OS?
I was not able to install it when I followed the instructions in Readme.txt...
Forum: Bioinformatics 07-13-2011, 04:26 PM
Replies: 20
Views: 10,093
Posted By joseph
I sent numerous e-mails to the authors, but still...

I sent numerous e-mails to the authors, but still no response.
Forum: Bioinformatics 02-25-2011, 08:29 AM
Replies: 11
Views: 8,353
Posted By joseph
help with Tophat's bowtie parameters

Hi
If it is not too much trouble, can you post a tophat file with modification to the the latest version (1.2). My data maps better when I set my own -n/--seedmms and -l/--seedlen parameters.
As...
Forum: Bioinformatics 02-17-2011, 10:33 AM
Replies: 2
Views: 4,252
Posted By joseph
cds

That solved the problem. Thank you for caring and answering my question.
Joseph
Forum: Bioinformatics 02-16-2011, 10:05 AM
Replies: 2
Views: 4,252
Posted By joseph
why cuffdiff cds-tests empty?

Hi

I ran cuffcompare with the reference annotation "refGene.gtf" which is RefSeq Genes (refGene) track from UCSC GB.

cuffcompare -V -r refGene.gtf -R -o s7_s8_refGene transcripts_s7.gtf...
Forum: Bioinformatics 02-12-2011, 06:46 PM
Replies: 8
Views: 4,518
Posted By joseph
how to get coverage from TopHat output?

Hi
the latest versions of TopHat do not generate the coverage.wig file. I used the file accepted_hits.bam with samsamtools and bedtools to generate a bedgraph.

samtools sort accepted_hits.bam...
Forum: Bioinformatics 10-13-2010, 09:01 AM
Replies: 2
Views: 2,106
Posted By joseph
bed file around the TSSs

Hi
I would highly appreciate if you could show me how to create a bed file around the TSSs from UCSC databases such as ensembl or refSeq genes. I need 350 nucleotides upstream and 150 nucleotides...
Forum: Bioinformatics 09-04-2010, 02:09 PM
Replies: 2
Views: 2,220
Posted By joseph
I used files separated with commas: ...

I used files separated with commas:

bowtie-build -f seq1.fa,seq2.fa,...,seqn.fa my_ebwt_base
Forum: Bioinformatics 09-04-2010, 12:50 PM
Replies: 2
Views: 2,220
Posted By joseph
maximum number of the reference input files for bowtie-build

Hi
Is there a maximum number of the reference input files for bowtie-build?
I am trying to build a Bowtie index from a set of 500 DNA sequences; I get the following error:
Error: could not open...
Forum: Bioinformatics 10-24-2009, 02:59 PM
Replies: 28
Views: 15,103
Posted By joseph
Andrea, have you tried bowtie to map the reads...

Andrea,
have you tried bowtie to map the reads to miRbase as you said? If you did, can you share your findings?
Forum: Bioinformatics 09-23-2009, 04:54 PM
Replies: 5
Views: 2,927
Posted By joseph
What would be the difference between the two...

What would be the difference between the two options (Tophat forcing Bowtie to do end-to-end mapping versus the default option of TopHat where the reads are split)? I am specifically interested in...
Forum: Bioinformatics 09-23-2009, 03:22 PM
Replies: 5
Views: 2,927
Posted By joseph
Actually, I heard from Cole that this parameter...

Actually, I heard from Cole that this parameter is controlled by TopHat, users cannot set it.
Forum: Illumina/Solexa 09-20-2009, 05:29 PM
Replies: 4
Views: 2,721
Posted By joseph
use TopHat, it breaks the 75 bp read into 3...

use TopHat, it breaks the 75 bp read into 3 segments. I heard TopHat does this to prevent the problem you mentionned, but I am not sure!
I hope Cole comments on this!
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