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Search: Posts Made By: FrankiB
Forum: Bioinformatics 04-07-2014, 09:35 AM
Replies: 7
Views: 9,952
Posted By FrankiB
Is it working with python 3.3 and if yes, where...

Is it working with python 3.3 and if yes, where can I find instructions for installation?
Forum: Bioinformatics 03-25-2014, 08:52 AM
Replies: 5
Views: 1,418
Posted By FrankiB
So for the whole genome, I do not need the...

So for the whole genome, I do not need the .intervals file in the input command line...
Forum: Bioinformatics 03-24-2014, 06:36 AM
Replies: 5
Views: 1,418
Posted By FrankiB
Ok. Thank you. But the command line to run...

Ok. Thank you.

But the command line to run FastaAlternateReferenceMaker requires a .intervals file (that one has been produced using the GATK pipeline) as input. Also I performed the variant...
Forum: Bioinformatics 03-21-2014, 06:58 AM
Replies: 5
Views: 1,418
Posted By FrankiB
How to append fasta files

Hi,

I have a series of snp and indels (csv format) for which I know the exact location on the the human genome (chromosome# and nucleotide position) and I would like to append the human genome...
Forum: Bioinformatics 02-20-2014, 10:05 AM
Replies: 7
Views: 4,673
Posted By FrankiB
Yes I see. Thank you very much

Yes I see. Thank you very much
Forum: Bioinformatics 02-20-2014, 07:38 AM
Replies: 7
Views: 4,673
Posted By FrankiB
Hi, Is it possible to get vcf output using...

Hi,

Is it possible to get vcf output using somatic mutation calling? If yes what should be the option in the command line?
Forum: General 02-13-2014, 12:14 PM
Replies: 2
Views: 1,076
Posted By FrankiB
Thank you very much

Thank you very much
Forum: General 02-13-2014, 11:00 AM
Replies: 2
Views: 1,076
Posted By FrankiB
How to call variants from two samples?

Hi,

I'm analyzing two exome deep sequencing libraries, one from cancer cells and the other from normal cells.
I have been through the GATK best practices to end with a recalibrated filtered vcf...
Forum: General 02-10-2014, 10:15 AM
Replies: 1
Views: 976
Posted By FrankiB
General question regarding GATK

Hi everybody,

I have a general question regarding variant calling using GATK. My question is maybe naive (or stupid) since I am new to NGS analysis...

I am half-way through my analysis using...
Forum: RNA Sequencing 02-07-2014, 08:31 AM
Replies: 2
Views: 1,643
Posted By FrankiB
Ok I see, thank you

Ok I see, thank you
Forum: RNA Sequencing 02-07-2014, 06:30 AM
Replies: 2
Views: 1,643
Posted By FrankiB
BWA -mem

Hi,

I'm using bwa-mem and how it is possible to know the percentage of reads mapped to the genome and all the stats?
Forum: General 01-29-2014, 08:31 AM
Replies: 31
Views: 14,331
Posted By FrankiB
Yea. bwa aln is working well (it seems). Now I'm...

Yea. bwa aln is working well (it seems). Now I'm running bwa sampe to combine the *.sai files.
Forum: General 01-29-2014, 08:06 AM
Replies: 31
Views: 14,331
Posted By FrankiB
Sorry to have mistaken you, but I have generated...

Sorry to have mistaken you, but I have generated the 5 files you are refering to.
Forum: General 01-29-2014, 07:34 AM
Replies: 31
Views: 14,331
Posted By FrankiB
I got about the same information: ...

I got about the same information:
@SQ SN:1 LN:249250621
@SQ SN:2 LN:243199373
@SQ SN:3 LN:198022430
@SQ SN:4 LN:191154276
@SQ SN:5 LN:180915260
@SQ SN:6 LN:171115067
@SQ SN:7 LN:159138663...
Forum: General 01-28-2014, 08:59 AM
Replies: 31
Views: 14,331
Posted By FrankiB
Yes I tried to allocated 7 gb and I got the same...

Yes I tried to allocated 7 gb and I got the same result...
Forum: General 01-28-2014, 08:49 AM
Replies: 31
Views: 14,331
Posted By FrankiB
Yes I'm using a 64-bit ansd 250 gb allocated for...

Yes I'm using a 64-bit ansd 250 gb allocated for VM.
Forum: General 01-28-2014, 07:36 AM
Replies: 31
Views: 14,331
Posted By FrankiB
No. I indexed it with the same version.

No. I indexed it with the same version.
Forum: General 01-28-2014, 07:34 AM
Replies: 31
Views: 14,331
Posted By FrankiB
I'm running on a PC using VMware wokstation and I...

I'm running on a PC using VMware wokstation and I allowed 4 gb.
Forum: General 01-28-2014, 07:27 AM
Replies: 31
Views: 14,331
Posted By FrankiB
I'm using the 0.7.5a version and I want to map on...

I'm using the 0.7.5a version and I want to map on the human genome g1k_V37. The index generated a couple of files and the biggest is around 3 gb.
Forum: General 01-28-2014, 07:02 AM
Replies: 31
Views: 14,331
Posted By FrankiB
BWA mem

Hi everybody,
I got this error from my first try using bwa mem. Is it a problem of memory?

[M::main_mem] read 82646 sequences (10000166 bp)...
Segmentation fault (core dumped)


Thank you...
Forum: Genomic Resequencing 01-22-2014, 06:36 AM
Replies: 11
Views: 10,396
Posted By FrankiB
OK thanks. But first I have to create the...

OK thanks.

But first I have to create the index. I'm using the human_g1k_v37 version. It has been 2 hours now that I've send the command and I have still this line:

[bwa_index] Pack FASTA...
...
Forum: Genomic Resequencing 01-20-2014, 10:32 AM
Replies: 11
Views: 10,396
Posted By FrankiB
What are the specific settings (options,...

What are the specific settings (options, parameters) to use when mapping RNA seq data on human genome using BWA software?
Forum: Bioinformatics 12-20-2013, 05:03 AM
Replies: 2
Views: 909
Posted By FrankiB
Unknown bases

Hi,

I'm new to deep sequencing analysis and I was wondering if there is a tool on Galaxy that can remove reads containing unknown bases (N).

Thanks for your time
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