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Forum: Academic/Non-Profit Jobs 11-12-2015, 12:52 AM
Replies: 0
Views: 629
Posted By tcezard
Bioinformatician position at Edinburgh Genomics

Description:
Edinburgh Genomics is a joint facility of the University of Edinburgh’s College of Medicine and Veterinary Medicine, and College of Science and Engineering, and a leading provider of...
Forum: Bioinformatics 04-18-2014, 02:33 AM
Replies: 34
Views: 17,833
Posted By tcezard
Hi Brian, That looks very interesting. Did...

Hi Brian,
That looks very interesting.
Did you do any test with Phix.
We routinely remove Phix read by aligning all reads the the reference.
Obviously Phix is very small so the chance of false...
Forum: Bioinformatics 04-16-2013, 06:28 AM
Replies: 6
Views: 1,705
Posted By tcezard
Can you be a bit more explicit about the tool you...

Can you be a bit more explicit about the tool you use?
How did you make the groups you're talking about?
Did you align the reads to your reference or did an actual MSA.
Forum: Bioinformatics 06-22-2010, 02:48 AM
Replies: 23
Views: 22,993
Posted By tcezard
I'm sure Heng li knows what he's talking about so...

I'm sure Heng li knows what he's talking about so you should check your commands and log messages, parameters used, maybe rerun the alignment command (and keep the command you're running).
If it...
Forum: Bioinformatics 06-22-2010, 02:12 AM
Replies: 23
Views: 22,993
Posted By tcezard
I'm wondering if you have unmapped read in your...

I'm wondering if you have unmapped read in your sam file to beggin with.

try
samtools view -bT ref.fa sam_file | samtools sort - bam_file
(with no .bam extension)
then
samtools flagstat...
Forum: Bioinformatics 06-22-2010, 01:45 AM
Replies: 23
Views: 22,993
Posted By tcezard
It should work ... Can you paste your commands...

It should work ...
Can you paste your commands and the first few lines of your sam file
Forum: Bioinformatics 06-21-2010, 07:50 AM
Replies: 23
Views: 22,993
Posted By tcezard
if you type samtools view -? you'll see...

if you type
samtools view -?

you'll see that to convert sam to bam you'll need the reference fasta file

2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'.

your command should...
Forum: Bioinformatics 04-26-2010, 04:39 AM
Replies: 191
Views: 77,725
Posted By tcezard
I believe I found a bug or I did not understand...

I believe I found a bug or I did not understand the documentation.
maybe there is a better place for bug report but I couldn't find a mailing list of bug tracker
My uderstanding of the Sequence...
Forum: Bioinformatics 04-22-2010, 02:35 AM
Replies: 27
Views: 10,647
Posted By tcezard
Thanks, That looks like a nice bit of software. ...

Thanks, That looks like a nice bit of software.
Just a question how does it handle CIGAR stretches of N in split read of RNA seq?

Thanks
Tim
Forum: Bioinformatics 04-02-2010, 04:08 AM
Replies: 2
Views: 4,563
Posted By tcezard
You should give a try to the UCSC liftover ...

You should give a try to the UCSC liftover
http://genome.ucsc.edu/cgi-bin/hgLiftOver
It lift from NCBI36.1 to GRCH37 but you can easily can the one that failed.
I don't know how different ...
Forum: Bioinformatics 03-23-2010, 03:27 AM
Replies: 5
Views: 2,036
Posted By tcezard
Have you tried Artemis. It can detect ORF and...

Have you tried Artemis.
It can detect ORF and annotate them and can read .bam file
http://www.sanger.ac.uk/resources/software/artemis/

Tim
Forum: Bioinformatics 02-24-2010, 10:07 AM
Replies: 4
Views: 2,094
Posted By tcezard
Don't know if it's relevent but I just read the...

Don't know if it's relevent but I just read the BWA for long read paper. you could have a look at that
http://bioinformatics.oxfordjournals.org/cgi/content/short/26/5/589?rss=1
Forum: Bioinformatics 02-24-2010, 09:13 AM
Replies: 4
Views: 2,094
Posted By tcezard
Blast would be an option and you can then use the...

Blast would be an option and you can then use the script blast2sam.pl from samtools to get the sam version and vizualise with IGV
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