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Forum: Bioinformatics 12-17-2012, 05:48 AM
Replies: 34
Views: 12,926
Posted By cjp
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, 09:57 AM
Replies: 34
Views: 12,926
Posted By cjp
This software worked OK on my 4GB workstation: ...

This software worked OK on my 4GB workstation:

http://www.hudsonalpha.org/gsl/software/bam2fastq.php

Chris
Forum: Bioinformatics 12-07-2011, 02:16 AM
Replies: 94
Views: 149,906
Posted By cjp
I think they are here (and other aligners'...

I think they are here (and other aligners' parameters too):

http://lh3lh3.users.sourceforge.net/alnROC.shtml

Chris
Forum: RNA Sequencing 12-06-2011, 08:50 AM
Replies: 4
Views: 2,646
Posted By cjp
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, 03:00 AM
Replies: 4
Views: 2,646
Posted By cjp
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, 06:36 AM
Replies: 8
Views: 4,349
Posted By cjp
There is a link here about making the picard dict...

There is a link here about making the picard dict file for GATK:

http://www.broadinstitute.org/gsa/wiki/index.php/Preparing_the_essential_GATK_input_files:_the_reference_genome

Download the...
Forum: Bioinformatics 12-05-2011, 05:36 AM
Replies: 8
Views: 4,349
Posted By cjp
The GATK command worked for me (did you make the...

The GATK command worked for me (did you make the picard ".dict" file for your reference fasta file?):

% java -Xmx2g -Djava.io.tmpdir=/path/to/tmp -jar...
Forum: RNA Sequencing 12-01-2011, 01:50 AM
Replies: 15
Views: 12,018
Posted By cjp
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, 12:17 PM
Replies: 15
Views: 12,018
Posted By cjp
Good idea - how well does TopHat cope if it needs...

Good idea - how well does TopHat cope if it needs to put two+ introns into an alignment - and thus align over 3 (or more) exons?

Chris
Forum: Bioinformatics 11-29-2011, 11:10 AM
Replies: 12
Views: 20,565
Posted By cjp
See this thread: ...

See this thread:

http://seqanswers.com/forums/showthread.php?t=2775

Chris
Forum: Bioinformatics 11-29-2011, 07:39 AM
Replies: 52
Views: 38,593
Posted By cjp
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, 02:51 AM
Replies: 19
Views: 12,327
Posted By cjp
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, 03:28 PM
Replies: 19
Views: 12,327
Posted By cjp
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, 11:33 AM
Replies: 2
Views: 3,228
Posted By cjp
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, 03:57 AM
Replies: 1
Views: 1,597
Posted By cjp
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, 03:40 AM
Replies: 5
Views: 2,426
Posted By cjp
You can install the EnsEMBL database on a local...

You can install the EnsEMBL database on a local Linux machine and get the API to see that, but am not sure if the VEP can be made to work on a local machine. The best place to ask is the mailing...
Forum: Bioinformatics 11-25-2011, 05:22 AM
Replies: 19
Views: 12,327
Posted By cjp
Maybe HTseq-count deals with counting spliced...

Maybe HTseq-count deals with counting spliced reads:

From this page:

http://www-huber.embl.de/users/anders/HTSeq/doc/count.html


"Make sure to use a splicing-aware aligner such as TopHat....
Forum: Bioinformatics 11-25-2011, 01:53 AM
Replies: 13
Views: 3,916
Posted By cjp
-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, 01:46 AM
Replies: 3
Views: 5,242
Posted By cjp
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, 09:58 AM
Replies: 13
Views: 3,916
Posted By cjp
Setting -g means you won't see any reads that...

Setting -g means you won't see any reads that align more than once as it sets both the -m and -k flags in Bowtie to 1:

-k <int> report up to <int> good alignments per read (default: 1)...
Forum: Bioinformatics 11-24-2011, 09:03 AM
Replies: 1
Views: 1,739
Posted By cjp
--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, 08:46 AM
Replies: 3
Views: 1,766
Posted By cjp
Maybe try here?: ...

Maybe try here?:

http://stats.stackexchange.com/
Forum: Bioinformatics 11-24-2011, 08:36 AM
Replies: 3
Views: 5,242
Posted By cjp
You'll only get duplicates in the BAM file if...

You'll only get duplicates in the BAM file if they are marked as duplicates. BWA doesn't mark them and samtools rmdup removes them. Try using picard MarkDuplicates

java -jar...
Forum: Bioinformatics 11-09-2011, 08:41 AM
Replies: 21
Views: 6,434
Posted By cjp
The headers look a bit different than normal -...

The headers look a bit different than normal - normally they end in /1 or /2

e.g.,

@HWUSI-EAS611_14:8:1:1489:931/1
and

@HWUSI-EAS611_14:8:1:1489:931/2

for the paired end data - note the...
Forum: Bioinformatics 11-09-2011, 08:34 AM
Replies: 21
Views: 6,434
Posted By cjp
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:
...
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