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Search: Posts Made By: poisson200
Forum: Bioinformatics 07-09-2011, 12:20 AM
Replies: 30
Views: 9,384
Posted By poisson200
Sounds very interesting as I am after a good...

Sounds very interesting as I am after a good "home" desktop as emergency back-up. What make/model and where buying please?

My experience with Corei7s is very positive; I have a 940 corei7 desktop...
Forum: Bioinformatics 07-08-2011, 11:56 PM
Replies: 4
Views: 2,439
Posted By poisson200
Hi. Interesting and confusing to me too. ...

Hi.
Interesting and confusing to me too.
Sam manual says that field five is the mapping quality; From manual;
field 5 = MAPQ Int [0,2^8-1] MAPping Quality

However and interestingly, the...
Forum: Bioinformatics 07-08-2011, 10:45 PM
Replies: 3
Views: 4,620
Posted By poisson200
Hi, Sorry, it was a while ago but I think I...

Hi,
Sorry, it was a while ago but I think I solved this by checking out latest version of GATK from cvs (rather than download the one from their website). Also...

# Needs the human genome to be...
Forum: Bioinformatics 06-30-2011, 02:56 AM
Replies: 1
Views: 3,657
Posted By poisson200
Question Bizzare

I got samtools to compile/work by explicitly setting the;

LIBPATH=/root/lib/libz.so.1.2.5

in the Makefile, which was inspired by
...
Forum: Bioinformatics 06-30-2011, 02:28 AM
Replies: 1
Views: 3,657
Posted By poisson200
Question samtools installation error; gzopen64

Dear All,
I have problem installing latest samtools. I posted to this thread, before realising it maybe better here.

Thanks for any help,

Link to thread with details. ...
Forum: RNA Sequencing 06-30-2011, 02:02 AM
Replies: 12
Views: 24,782
Posted By poisson200
Unhappy Painful

Dear all,
I have a similar issue on a Centos machine. I want to compile samtools and it runs fine until it issues this;
gcc -g -Wall -O2 -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o...
Forum: Bioinformatics 06-27-2011, 04:38 AM
Replies: 5
Views: 3,357
Posted By poisson200
Thank you for your replies and advice. ...

Thank you for your replies and advice.
Interesting what you say about NCBI gene id, as this is a number (if you mean Gene Entrez ID). I have not seen many manuscripts that report genes in abstracts...
Forum: Bioinformatics 06-26-2011, 04:29 AM
Replies: 5
Views: 3,357
Posted By poisson200
Smile What should be included to make a good transcriptome/RNA-seq paper?

Dear All,
I have done analyses on RNA-seq data that finds putative isoforms, differentially expressed genes/isoforms and gives a more complete picture of a tissues transcriptome.

I was wondering...
Forum: Bioinformatics 06-24-2011, 11:17 AM
Replies: 12
Views: 6,765
Posted By poisson200
Hi All, If you don't know already, you can...

Hi All,
If you don't know already, you can submit your cuffdiff problems to tophat.cufflinks@gmail.com
Forum: Bioinformatics 06-24-2011, 03:35 AM
Replies: 3
Views: 4,230
Posted By poisson200
Hello there, I had a problem mapping paired...

Hello there,
I had a problem mapping paired end data with bowtie. In the bowtie manual it is thought that the paired ends from colourspace are in the forward strand- forward strand --ff orientation...
Forum: Bioinformatics 06-24-2011, 03:21 AM
Replies: 6
Views: 5,195
Posted By poisson200
Possible alternatives

It is possible you could remove errors in colour-space reads by first

1) running SAET from bioscope
2) Running Sasson and Michael Solid read quality scripts. (PMID: 20207696)

then running...
Forum: Bioinformatics 06-24-2011, 03:13 AM
Replies: 8
Views: 3,440
Posted By poisson200
Dear Richard, Thanks for the feedback. I think...

Dear Richard,
Thanks for the feedback. I think for things like mutation detection, this hard/soft clipping could be OK as long as the read does not map to many locations in the genome. However, for...
Forum: Bioinformatics 06-23-2011, 08:11 AM
Replies: 1
Views: 6,130
Posted By poisson200
You can try installing BEDTools and using bedToBam

You can try installing BEDTools and using bedToBam
Forum: Bioinformatics 06-23-2011, 07:41 AM
Replies: 8
Views: 3,440
Posted By poisson200
Re-open bowtie vs. bioscope mapping

Dear all,
I am wondering about the meaning of bioscope mapping. H in a cigar string means "hard clipped" as far as I can see. Therefore, a lot of the alignments below are clipped at the beginning of...
Forum: Bioinformatics 06-17-2011, 02:30 AM
Replies: 3
Views: 3,493
Posted By poisson200
Hi. You may want to try the Bioconductor...

Hi.
You may want to try the Bioconductor mailing list if you have not already and ask there.
https://stat.ethz.ch/mailman/listinfo/bioconductor

If you don't find an answer. You could find all...
Forum: Bioinformatics 06-16-2011, 02:09 PM
Replies: 6
Views: 6,176
Posted By poisson200
Hi Peter. Thanks for answering anyway. I found...

Hi Peter.
Thanks for answering anyway. I found a subsequent error anyway :-).

John.
Forum: Bioinformatics 06-16-2011, 02:06 PM
Replies: 0
Views: 1,206
Posted By poisson200
Unhappy Failures to submit errors to http://getsatisfaction.com/gsa

Has anyone else had problems submitting to http://getsatisfaction.com/gsa?

I am able to log in but once I try and submit an error report as per my earlier post, I keep getting bad requests html...
Forum: Bioinformatics 06-16-2011, 11:56 AM
Replies: 3
Views: 4,620
Posted By poisson200
GATK error

java -jar gatk -T IndelGenotyperV2 -l INFO -bed brief.bed -R /data/results/genomes/hg18/hg18.fa -I fastq.sorted.realigned.bam -o fastq_indel.txt -verbose fastq_indel_statistics.txt

This produces...
Forum: Bioinformatics 06-16-2011, 08:58 AM
Replies: 6
Views: 6,176
Posted By poisson200
Answer is...

Use CreateSequenceDictionary.jar
:D
Forum: Bioinformatics 06-16-2011, 08:26 AM
Replies: 6
Views: 6,176
Posted By poisson200
Picard and GATK

Dear samtools,
I am using Picard to re-order human chromosomes since GATK is not able to handle different ordering.

GATK advises me to use the Picard utility picard-tools-1.47/ReorderSam.jar
...
Forum: Bioinformatics 04-15-2011, 07:47 AM
Replies: 7
Views: 15,660
Posted By poisson200
Thank you for your answers Sorry, I...

Thank you for your answers



Sorry, I knew this; I already use bb's but was lazy in precisely conveying it. :o

OK, I will try out your suggestions. Thanks.

Kind regards,
Forum: Bioinformatics 04-15-2011, 06:44 AM
Replies: 7
Views: 15,660
Posted By poisson200
Displaying a custom track of transcripts from cufflinks

Dear Bioinformaticians,
Please can you tell me how to display a full genomes/transcriptomes worth of transcripts in the hg19 UCSC genome browser?

I make the assumption that a full transcriptome...
Forum: Bioinformatics 04-06-2011, 06:29 AM
Replies: 191
Views: 76,577
Posted By poisson200
Hi Markus, Simon. Markus, I had a slightly...

Hi Markus, Simon.
Markus, I had a slightly different point, htseq is working for me but some genes would have a count of 0 if the GTF file had a gene fusion annotation.

In the GTF there is...
Forum: Bioinformatics 04-01-2011, 12:03 PM
Replies: 2
Views: 14,076
Posted By poisson200
Dear Aurelien, Your post is very interesting...

Dear Aurelien,
Your post is very interesting and I would, too, like to understand fully the output of cufflinks/compare/diff. The one thing that caught my eye is that you have got p_id's in your...
Forum: Bioinformatics 04-01-2011, 06:00 AM
Replies: 191
Views: 76,577
Posted By poisson200
htseq-count; a small consideration/nice to have

Dear Simon,
I have been doing some testing regards counts of reads to genes based on genome mapping.

My GTF file is from hg19 Genome Browser for Refseq gene (table browser).
Reads are FASTQ...
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