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Forum: Illumina/Solexa 05-24-2012, 02:51 AM
Replies: 82
Views: 131,448
Posted By nicolallias
What's now ? My last update on this situation is...

What's now ? My last update on this situation is this link (http://www.genengnews.com/gen-news-highlights/b-illumina-b-shuns-b-roche-b-s-improved-acquisition-offer-of-6-5b/81246581/)
Forum: Bioinformatics 03-24-2011, 01:50 AM
Replies: 7
Views: 3,481
Posted By nicolallias
Smile Not if the fastq is generated with line wrapping...

Not if the fastq is generated with line wrapping - I've seen one of the bwa tool, qualfa2fq.pl doing this on the quality.

But you may overestimate the number of reads if the fastq is encoding...
Forum: Bioinformatics 03-22-2011, 12:52 AM
Replies: 6
Views: 2,545
Posted By nicolallias
From a sff you can extract (even on a Windows)...

From a sff you can extract (even on a Windows) fasta and quality files with sff_extract (http://seqanswers.com/forums/showpost.php?p=14687&postcount=2).
You may also have a look on this page this...
Forum: Bioinformatics 03-21-2011, 02:16 AM
Replies: 2
Views: 1,566
Posted By nicolallias
Wich is your python version ? python -V ...

Wich is your python version ?
python -V

Edit: I think you are alternatively using 2 python versions:
- one older than 2.3 (which haven't the set command)
- another more recent (works)
I had...
Forum: Bioinformatics 03-17-2011, 06:21 AM
Replies: 3
Views: 9,032
Posted By nicolallias
Hi, Look at the second column, the CIGAR line,...

Hi,
Look at the second column, the CIGAR line, set its values in http://picard.sourceforge.net/explain-flags.html

You can also use in command line
smatools view -X
Forum: Bioinformatics 03-09-2011, 05:55 AM
Replies: 4
Views: 2,699
Posted By nicolallias
From tophat manual: --closure-search ...

From tophat manual:

--closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (<=...
Forum: Bioinformatics 03-09-2011, 05:31 AM
Replies: 10
Views: 8,211
Posted By nicolallias
Sorry, now I get it... Me neither :confused:...

Sorry, now I get it...

Me neither :confused:

Anyway, you could pipe with a
awk '{print $1" "$2" "$3" "$4" "$5" "$6" "NR" "$7}'
Forum: Illumina/Solexa 03-09-2011, 01:41 AM
Replies: 6
Views: 5,405
Posted By nicolallias
From http://bio-bwa.sourceforge.net/bwa.shtml ...

From http://bio-bwa.sourceforge.net/bwa.shtml


How wrong, messy ? Could you paste here a short example ?
Forum: Bioinformatics 03-09-2011, 01:11 AM
Replies: 10
Views: 8,211
Posted By nicolallias
Hi, You want the second best blast hit ? If so,...

Hi,
You want the second best blast hit ? If so, no need to count the rank, just use a shell command :
head -n 2 blast_output.m8 | tail -n 1
(in fact, change 2 by the position of the line you want)...
Forum: Bioinformatics 03-02-2011, 08:16 AM
Replies: 5
Views: 3,479
Posted By nicolallias
I think so.

I think so.
Forum: Bioinformatics 03-02-2011, 06:59 AM
Replies: 5
Views: 3,479
Posted By nicolallias
Sam flags have the same meaning whatever software...

Sam flags have the same meaning whatever software produced it.
But I can be wrong :s

If I'm right, you're looking something like http://picard.sourceforge.net/explain-flags.html

On another...
Forum: Bioinformatics 02-25-2011, 05:15 AM
Replies: 12
Views: 6,590
Posted By nicolallias
cuffdiff v0.9.3 seg. fault

Hello everyone,
I've found another way (maybe linked with your problem) to get the "Segmentation fault":

cuffdiff -o ./ input.gtf input1.bam input2.bam

works fine, but

cuffdiff -o...
Forum: Bioinformatics 12-01-2010, 05:02 AM
Replies: 8
Views: 2,157
Posted By nicolallias
Exact, and using already written tools is your...

Exact, and using already written tools is your best option.
angelpie: if you wish to learn more, you really should visit the wikipedia page about Fastq format...
Forum: Bioinformatics 12-01-2010, 01:04 AM
Replies: 8
Views: 2,157
Posted By nicolallias
Hi, The only difference between those formats...

Hi,
The only difference between those formats is the quality, if you are familiar with Perl, try the following :
http://seqanswers.com/forums/showthread.php?t=5192
$q_line =~...
Forum: Bioinformatics 12-01-2010, 12:57 AM
Replies: 6
Views: 3,402
Posted By nicolallias
Hi, Play with :...

Hi,
Play with : http://picard.sourceforge.net/explain-flags.html
163(=1+2+32+ 128) is in decimal
0x00.. are hexadecimal (base 16, not 10)

0,0010 is equivalent to the decimal 16^1 so 16.
Forum: 454 Pyrosequencing 10-29-2010, 12:16 AM
Replies: 6
Views: 2,840
Posted By nicolallias
Unhappy Some news : the matter seems to be located on the...

Some news : the matter seems to be located on the sff file generation...
Forum: 454 Pyrosequencing 10-22-2010, 01:45 AM
Replies: 6
Views: 2,840
Posted By nicolallias
The problem seems to be the sff file, software...

The problem seems to be the sff file, software developers at 454 are working on this.
Hope some good news soon ;-)
Forum: 454 Pyrosequencing 10-18-2010, 01:21 AM
Replies: 6
Views: 2,840
Posted By nicolallias
Yes :( I will do that. Edit: Both...

Yes :(

I will do that.

Edit: Both alignments on sff and fasta have been proceeded on E.coli, both gave ace and fna files full of contigs. But I won't look after the best method (fasta or sff)...
Forum: 454 Pyrosequencing 10-14-2010, 03:40 AM
Replies: 6
Views: 2,840
Posted By nicolallias
Hi flxlex, I'm considering de novo assemblies...

Hi flxlex,
I'm considering de novo assemblies only, these observations are based on the study of dozens of assemblies done with Newbler 2.3 and this problem occurs:
- on gDNA from bacteria
- on...
Forum: 454 Pyrosequencing 10-13-2010, 01:58 AM
Replies: 6
Views: 2,840
Posted By nicolallias
gsAssembly (Newbler) de novo behaviour, inputs and outputs

Hello there,
It appears that the content of the ACE file is quite inconsistent with the fasta files content and the 454NewblerMetrics file:
Sometimes, the fna files are empty, 454NewblerMetrics has...
Forum: Core Facilities 08-24-2010, 01:16 AM
Replies: 2
Views: 3,739
Posted By nicolallias
Thanks for your reply :)

Thanks for your reply :)
Forum: Core Facilities 08-18-2010, 07:21 AM
Replies: 2
Views: 3,739
Posted By nicolallias
Illumina samplesheet fields

Hi there,

A samplesheet (for demultiplexer.pl) as the following headers:
FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator

What is "Recipe" meaning ? :confused:

Thanks
Forum: Bioinformatics 05-10-2010, 12:20 AM
Replies: 19
Views: 11,055
Posted By nicolallias
Can I ave a look to your script ? Thanks :) ...

Can I ave a look to your script ?
Thanks :)

nico l'allias
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