Forum: Bioinformatics
12-17-2012, 04:48 AM
|
|
Replies: 34
Views: 15,591
Hi,
It worked for me.
% tar -xvzf...
Hi,
It worked for me.
% tar -xvzf bam2fastq-1.1.0.tgz
bam2fastq-1.1.0/
bam2fastq-1.1.0/bam2fastq.cpp
bam2fastq-1.1.0/HISTORY.txt
bam2fastq-1.1.0/LICENSE
|
|
Forum: Bioinformatics
12-21-2011, 08:57 AM
|
|
Replies: 34
Views: 15,591
|
|
Forum: Bioinformatics
12-07-2011, 01:16 AM
|
|
Replies: 93
Views: 175,830
|
|
Forum: RNA Sequencing
12-06-2011, 07:50 AM
|
|
Replies: 4
Views: 3,317
Thanks for that Tom,
A bit later, I also...
Thanks for that Tom,
A bit later, I also found some other links where other users that had different command line options:
http://openwetware.org/wiki/Wikiomics%3aRNA-Seq#GMAP.2FGSNAP
...
|
|
Forum: RNA Sequencing
12-06-2011, 02:00 AM
|
|
Replies: 4
Views: 3,317
Hi Thomas,
I'm trying to look at both RUM...
Hi Thomas,
I'm trying to look at both RUM and gsnap for RNA-seq alignments and compare to TopHat. gsnap looks like really nice software and I noticed user lh3 recommended it! What command line...
|
|
Forum: Bioinformatics
12-05-2011, 05:36 AM
|
|
Replies: 8
Views: 5,317
|
|
Forum: Bioinformatics
12-05-2011, 04:36 AM
|
|
Replies: 8
Views: 5,317
|
|
Forum: RNA Sequencing
12-01-2011, 12:50 AM
|
|
Replies: 15
Views: 13,457
Also try adding --closure-search to tophat for...
Also try adding --closure-search to tophat for reads with a small insert size:
--closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used...
|
|
Forum: RNA Sequencing
11-30-2011, 11:17 AM
|
|
Replies: 15
Views: 13,457
|
|
Forum: Bioinformatics
11-29-2011, 10:10 AM
|
|
Replies: 12
Views: 23,283
|
|
Forum: Bioinformatics
11-29-2011, 06:39 AM
|
|
Replies: 52
Views: 43,872
Hi Simon,
Thanks for the helpful comments in...
Hi Simon,
Thanks for the helpful comments in this thread!
But, I was reading the whole thread from the beginning - and maybe you should edit the post - number 31 - to say you noticed later it...
|
|
Forum: Bioinformatics
11-29-2011, 01:51 AM
|
|
Replies: 19
Views: 15,003
Yes is a two-issue thread!
The samtools...
Yes is a two-issue thread!
The samtools thing is that mpileup adds '>' and '<' symbols where the cigar part of an alignment is an N. You can use "samtools depth" and that gives me 0 over introns.
|
|
Forum: Bioinformatics
11-28-2011, 02:28 PM
|
|
Replies: 19
Views: 15,003
Hi adameur,
I'd thought to mention your...
Hi adameur,
I'd thought to mention your paper in my previous answer as well!
Do you know how much it may affect mRNA-seq studies - where people try to select processed RNA's from total RNA...
|
|
Forum: Bioinformatics
11-28-2011, 10:33 AM
|
|
Replies: 2
Views: 4,108
Copied and pasted from my previous answer to...
Copied and pasted from my previous answer to debug failed TopHat runs: http://seqanswers.com/forums/showthread.php?t=14140
When debugging failed TopHat runs, you can also try to run the individual...
|
|
Forum: Bioinformatics
11-28-2011, 02:57 AM
|
|
Replies: 1
Views: 2,207
In here for 133 - the samtools flags:...
In here for 133 - the samtools flags: http://picard.sourceforge.net/explain-flags.html
you get:
Summary:
read paired
read unmapped
second in pair
So the read is unmapped:
|
|
Forum: Bioinformatics
11-28-2011, 02:40 AM
|
|
Replies: 5
Views: 3,277
|
|
Forum: Bioinformatics
11-25-2011, 04:22 AM
|
|
Replies: 19
Views: 15,003
|
|
Forum: Bioinformatics
11-25-2011, 12:53 AM
|
|
Replies: 13
Views: 5,341
-Q is usually for SOLiD colour-space.
When...
-Q is usually for SOLiD colour-space.
When debugging failed TopHat runs, you can also try to run the individual commands from the command line yourself.
In the logs/ sub-directory of your...
|
|
Forum: Bioinformatics
11-25-2011, 12:46 AM
|
|
Replies: 3
Views: 6,823
It looks for reads that have the same start...
It looks for reads that have the same start position and then keeps the best one based on sequence quality scores - it's a fairly basic approach. Also look at this thread which recommends to use...
|
|
Forum: Bioinformatics
11-24-2011, 08:58 AM
|
|
Replies: 13
Views: 5,341
|
|
Forum: Bioinformatics
11-24-2011, 08:03 AM
|
|
Replies: 1
Views: 2,492
--initial-read-mismatches and...
--initial-read-mismatches and --segment-mismatches are the two values passed to "bowtie -n" or "bowtie -v" at different Bowtie searches in the TopHat pipeline. I'm not sure you can control the -l or...
|
|
Forum: Bioinformatics
11-24-2011, 07:46 AM
|
|
Replies: 3
Views: 2,384
|
|
Forum: Bioinformatics
11-24-2011, 07:36 AM
|
|
Replies: 3
Views: 6,823
|
|
Forum: Bioinformatics
11-09-2011, 07:41 AM
|
|
Replies: 21
Views: 8,004
|
|
Forum: Bioinformatics
11-09-2011, 07:34 AM
|
|
Replies: 21
Views: 8,004
Did you try other aligners such as BWA or...
Did you try other aligners such as BWA or Bowtie2. They are much better at pairing reads. Bowtie2 is easy to run and pretty quick too, but you'll need to reindex your genome.
example command:
...
|
