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Search: Posts Made By: tdm
Forum: Bioinformatics 10-31-2012, 12:10 PM
Replies: 0
Views: 1,032
Posted By tdm
big variant database: do you want to share?

Hello,
I am beguining to build a database with all our SNPs and indels from NGS and micrarrays. Here are our current need :
- the variants will be annoted (gerp, sift, polyphen...)
- they will be...
Forum: SOLiD 03-31-2011, 09:02 AM
Replies: 10
Views: 4,037
Posted By tdm
Hi niceday With SOLID protocol, it is not...

Hi niceday

With SOLID protocol, it is not possible to go into enrichment without PCR because adapters are truncated and we need the nick translation step to attach correctly the adpaters.
thank...
Forum: SOLiD 03-31-2011, 05:19 AM
Replies: 10
Views: 4,037
Posted By tdm
I should be able to figure something with...

I should be able to figure something with coordinates in color cfasta file.
thank you
thibault
Forum: SOLiD 03-30-2011, 01:56 PM
Replies: 10
Views: 4,037
Posted By tdm
I was already thinking about the point number 2. ...

I was already thinking about the point number 2.
I will check about distance between the duplicate of same fragment.
Do you know if picard argument OPTICAL_DUPLICATE_PIXEL_DISTANCE work with SOLID...
Forum: SOLiD 03-30-2011, 12:55 PM
Replies: 10
Views: 4,037
Posted By tdm
Hi PMiguel, I have the data you ask for: Type...

Hi PMiguel,
I have the data you ask for:
Type of library: SureSelect All Human Exon Capture (50Mb)
Sequencing: Fragment (50bp), barcoded samples, 6 samples/slide
How many cycles of PCR: As low as...
Forum: SOLiD 03-30-2011, 11:37 AM
Replies: 10
Views: 4,037
Posted By tdm
PCR duplicates increase when excess of beads

Hello,
We are experiencing an increasing of PCR duplicates.
Could this be realated to an increasing of the quantity of beads in order to get more reads?
Thibault
Forum: Bioinformatics 01-31-2011, 01:58 PM
Replies: 0
Views: 1,879
Posted By tdm
cuffdiff: same run but different FPKM, your thoughts?

Hello,
I was wondering how cuffdiff would differ if I run it on the same data.
Here are the fpkm of 4 runs for a gene: 38.2168 2.50089 32.3986 39.0589
Same runs about another gene: 46.8446...
Forum: SOLiD 12-10-2010, 08:54 AM
Replies: 9
Views: 3,355
Posted By tdm
That is why i would just prefix by 1 or 2 the...

That is why i would just prefix by 1 or 2 the headers, depending on the run (1st or 2nd). So i will be sure it is ok.
Forum: SOLiD 12-10-2010, 08:28 AM
Replies: 9
Views: 3,355
Posted By tdm
Thx Westerman, This was my 1st thought. ...

Thx Westerman,
This was my 1st thought.
Merging sam files is faster, but merging qual and csfasta files makes more sense to me.
So if i prefix fasta names by 1_ for the 1st run, and 2_ for second...
Forum: SOLiD 12-10-2010, 06:27 AM
Replies: 9
Views: 3,355
Posted By tdm
perfect :) I will try that next weekend. Thx...

perfect :)
I will try that next weekend.
Thx for your help !
Forum: SOLiD 12-09-2010, 09:51 AM
Replies: 9
Views: 3,355
Posted By tdm
Thx for your answer :) there won't be any...

Thx for your answer :)
there won't be any quality or score values bias ?
Forum: SOLiD 12-09-2010, 09:28 AM
Replies: 9
Views: 3,355
Posted By tdm
Can we merge 2 csfasta files ?

Hello,
I would like to merge 2 csfasta reads files:
We have performed a poor sequencing.
We re-did the sequencing.
Now we want to run the mapping software on this 2 read sets together in order to...
Forum: Bioinformatics 11-19-2010, 06:04 AM
Replies: 6
Views: 2,118
Posted By tdm
From source code, its the minimum read length....

From source code, its the minimum read length. There is also a maximum, but not displayed. I think it is alright.
Forum: Bioinformatics 11-17-2010, 08:45 AM
Replies: 6
Views: 2,118
Posted By tdm
I have the same message, cufflinks 092 and...

I have the same message, cufflinks 092 and bioscope 1.2
Maybe it is just a typing error with the message about read type.
Forum: Bioinformatics 11-16-2010, 01:09 PM
Replies: 2
Views: 2,143
Posted By tdm
No, there was no testing data coming with the...

No, there was no testing data coming with the tool. SO i assume maybe indel was lookin for an information not present.
I had an issue like that with samtools looking for XS information, but last...
Forum: Bioinformatics 11-16-2010, 12:03 PM
Replies: 2
Views: 2,143
Posted By tdm
dindel and bioscop: someone did it?

Hello,
I am using bioscope to align reads (solid), and get a bam file with matobam tool from this software.
I wanted to try dindel and compare results with the build in plugin, but I did not get...
Forum: Bioinformatics 10-19-2010, 11:41 AM
Replies: 6
Views: 2,118
Posted By tdm
bioscope single read BAM & Cufflinks

Dear Adam,
I would like to know to what extend is the compatibility with bioscope bam files ?
I produce BAM files with the single read pipeline, but Cufflinks still bother me with XS attribute.
...
Forum: Bioinformatics 09-30-2010, 12:27 PM
Replies: 18
Views: 5,087
Posted By tdm
THe problem for which i open this discussion was...

THe problem for which i open this discussion was solved with the updated version of cufflinks.
Thanks :)
Forum: Bioinformatics 09-28-2010, 08:23 AM
Replies: 18
Views: 5,087
Posted By tdm
Have you tried cufflinks 0.9.0 beta ?

Hello,
I wanted to try and compare my results with the previous version, but with the same options and the same set of data, i got an error:
$ cufflinks_09 wt.sr.corrected.sam.sorted
cufflinks_09:...
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