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Search: Posts Made By: jeny
Forum: Bioinformatics 12-27-2011, 04:43 AM
Replies: 7
Views: 4,440
Posted By jeny
I am not sure if it could do what you want, but...

I am not sure if it could do what you want, but have you tried variant_effect_predistor of Ensembl http://www.ensembl.org/tools.html?
Forum: Bioinformatics 12-26-2011, 03:11 AM
Replies: 4
Views: 2,183
Posted By jeny
Do you have the index bam file corresponding to...

Do you have the index bam file corresponding to your bam in the same directory?
For troubleshooting, perl version of BreakDancerMax is helpful. Error message are more clear than C version.
Hope...
Forum: Bioinformatics 09-22-2011, 05:28 AM
Replies: 366
Views: 193,628
Posted By jeny
ok, thanks for your quick reply. I will install...

ok, thanks for your quick reply.
I will install latest jre.
Cheers
Forum: Bioinformatics 09-22-2011, 05:02 AM
Replies: 366
Views: 193,628
Posted By jeny
I downloaded latest FastQC version to analyze...

I downloaded latest FastQC version to analyze fastq generated by CASAVA1.8 pipeline.
But running it on PhiX data returned message :
...
Approx 95% complete for PhiX_NoIndex_L008_R1.fastq.gz...
Forum: Bioinformatics 06-30-2011, 07:15 AM
Replies: 7
Views: 5,254
Posted By jeny
there is a script export2sam.pl in samtools...

there is a script export2sam.pl in samtools package (opensource) that may help you.
Forum: Illumina/Solexa 05-25-2011, 11:20 PM
Replies: 1
Views: 1,761
Posted By jeny
I suggest you have a look to export2sam.pl...

I suggest you have a look to export2sam.pl script.
In this file you could find a section "quality value conversion table" explaining quality format start point and end point.
So you could know...
Forum: Bioinformatics 01-25-2011, 07:33 AM
Replies: 89
Views: 65,429
Posted By jeny
In my point of view there are goods changes and i...

In my point of view there are goods changes and i am happy to learn about this new version.
But, why doesn't illumina make aware its users about these changes (simply by mail)? Information is badly...
Forum: Bioinformatics 12-29-2010, 12:46 AM
Replies: 4
Views: 2,951
Posted By jeny
Hi Tirza, I commented lines that you...

Hi Tirza,

I commented lines that you suggested and it works.

Many thanks,
Jennifer
Forum: Bioinformatics 12-28-2010, 01:39 AM
Replies: 4
Views: 2,951
Posted By jeny
Fastxtoolkit nucleotide distribution issue

Hi all,
I need some help on fastx-toolkit use.
I would like to generate nucleotide distribution line graph but I don't manage.
Below is command lines that I used :
1-to obtain statistics report...
Forum: Bioinformatics 11-15-2010, 07:33 AM
Replies: 10
Views: 6,371
Posted By jeny
Hi, I asked this to illumina techsupport a...

Hi,

I asked this to illumina techsupport a while ago, and their answer was :
The BCL converter doesn't allow you to specify lanes. I would strongly recommend not to split a RunFolder apart until...
Forum: Bioinformatics 10-07-2010, 03:52 AM
Replies: 14
Views: 3,711
Posted By jeny
Hi Gavin, did you try to view the alignment...

Hi Gavin,
did you try to view the alignment using an other third part tool ?
If I suggest you that, it is because I had the same problem with my SAM files, and this problem reproduced with other...
Forum: Bioinformatics 09-10-2010, 01:20 AM
Replies: 1
Views: 4,326
Posted By jeny
Hi, I have not tried it for the moment, but...

Hi,

I have not tried it for the moment, but you could use CASAVA-1.7 and samtools to do this.
1 - run GEARLD analysis with the option ''WITH_SORTED'' into config.txt file
2 - install samtools
3...
Forum: Bioinformatics 06-18-2010, 01:02 AM
Replies: 3
Views: 2,781
Posted By jeny
Hi DougB, I am interested in supersplat. I...

Hi DougB,

I am interested in supersplat.
I run it with parameters -c 4 and -i 15, on a dataset of 21461960 unique reads and 3584 reference sequences (there are scaffolds).
superslpat processed...
Forum: Bioinformatics 03-10-2010, 07:16 AM
Replies: 123
Views: 44,802
Posted By jeny
Hi Iain, you are right. The problem is that...

Hi Iain,

you are right. The problem is that s_N_export.txt or s_N_sorted.txt files contain chromosome matched (or genome) and not contig name. So, in fact Tablet can't match chromosome (in export...
Forum: Bioinformatics 03-10-2010, 05:43 AM
Replies: 123
Views: 44,802
Posted By jeny
Hi all, I am working on Illumina GAIIx...

Hi all,

I am working on Illumina GAIIx single read data.
To test Tablet, I used NSTbioinformatics sorted2sam.pl script on my data (s_N_sorted.txt) to generate s_N_sorted.sam (SAM format). That...
Forum: Introductions 03-08-2010, 07:17 AM
Replies: 373
Views: 136,315
Posted By jeny
Hi all, I am a bioinformatician and I...

Hi all,

I am a bioinformatician and I started to work on illumina GAiix last week.
I will have in charge : data storage, software tests, and data analysis.
I think this forum will be helpfull !...
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