Forum: Bioinformatics
04-07-2014, 10:35 AM
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Replies: 7
Views: 10,514
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Forum: Bioinformatics
03-25-2014, 09:52 AM
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Replies: 5
Views: 1,747
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Forum: Bioinformatics
03-24-2014, 07:36 AM
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Replies: 5
Views: 1,747
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...
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Forum: Bioinformatics
03-21-2014, 07:58 AM
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Replies: 5
Views: 1,747
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...
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Forum: Bioinformatics
02-20-2014, 11:05 AM
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Replies: 7
Views: 5,161
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Forum: Bioinformatics
02-20-2014, 08:38 AM
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Replies: 7
Views: 5,161
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Forum: General
02-13-2014, 01:14 PM
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Replies: 2
Views: 1,330
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Forum: General
02-13-2014, 12:00 PM
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Replies: 2
Views: 1,330
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...
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Forum: General
02-10-2014, 11:15 AM
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Replies: 1
Views: 1,146
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...
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Forum: RNA Sequencing
02-07-2014, 09:31 AM
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Replies: 2
Views: 1,979
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Forum: RNA Sequencing
02-07-2014, 07:30 AM
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Replies: 2
Views: 1,979
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?
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Forum: General
01-29-2014, 09:31 AM
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Replies: 31
Views: 15,623
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Forum: General
01-29-2014, 09:06 AM
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Replies: 31
Views: 15,623
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Forum: General
01-29-2014, 08:34 AM
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Replies: 31
Views: 15,623
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...
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Forum: General
01-28-2014, 09:59 AM
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Replies: 31
Views: 15,623
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Forum: General
01-28-2014, 09:49 AM
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Replies: 31
Views: 15,623
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Forum: General
01-28-2014, 08:36 AM
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Replies: 31
Views: 15,623
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Forum: General
01-28-2014, 08:34 AM
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Replies: 31
Views: 15,623
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Forum: General
01-28-2014, 08:27 AM
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Replies: 31
Views: 15,623
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Forum: General
01-28-2014, 08:02 AM
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Replies: 31
Views: 15,623
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...
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Forum: Genomic Resequencing
01-22-2014, 07:36 AM
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Replies: 11
Views: 11,540
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...
...
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Forum: Genomic Resequencing
01-20-2014, 11:32 AM
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Replies: 11
Views: 11,540
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Forum: Bioinformatics
12-20-2013, 06:03 AM
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Replies: 2
Views: 1,090
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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