Forum: Bioinformatics
03-23-2016, 03:06 AM
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Replies: 1
Views: 6,052
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Forum: Bioinformatics
07-04-2014, 03:09 AM
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Replies: 0
Views: 927
denovogear parameter
I'm trying to use denovogear to extract de novo variants from exome trios. Anyone can explain me the difference in the output parameter?
tgt_null/tgt_dnm
pp_null/pp_dnm
What parameter I have to...
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Forum: Bioinformatics
09-25-2013, 05:13 AM
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Replies: 1
Views: 1,503
ngsrich error coverage
Dear, i'm computing the coverage of a whole exome.
I run NGSrich as:
> java NGSrich evaluate -r file.bam.sorted.bam -u hg19 -a refGene.txt -t designwes.bed -o outputdir -s name
and the...
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Forum: Bioinformatics
07-08-2013, 09:38 AM
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Replies: 9
Views: 7,262
analysis amplicon miseq
Dear,
I sequenced 5 genes using truseq custom amplicon kit on Miseq. But if I process the data using bwa + samtools, the results seem to be not good.
Anyone has any idea about the pipeline of...
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Forum: Bioinformatics
07-08-2013, 08:44 AM
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Replies: 13
Views: 11,017
the problem is the index of genome.fasta
if I...
the problem is the index of genome.fasta
if I use bwa0.6.2 for sampe, it returns me:
[bns_restore_core] fail to open file '/dati1/reference/genomes/hg19.fasta.nt.ann'. Abort!
i have tried to...
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Forum: Bioinformatics
07-08-2013, 06:08 AM
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Replies: 13
Views: 11,017
bwa sampe error
Dear,
I run BWA 0.7.5a
>bwa aln genome.fasta read1.fastq > read1.sai
>bwa aln genome.fasta read2.fastq > read2.sai
> bwa sampe -r '@RG\tID:s\tLB:ss\tPL:ILLUMINA\tPU:l1\tSM:' genome.fasta...
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Forum: Bioinformatics
04-23-2013, 02:41 AM
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Replies: 2
Views: 1,488
I use bwa, samtools rmdup to remove duplicates...
I use bwa, samtools rmdup to remove duplicates (not -S option), gatk for local realignment and recalibration.
The reads before alignment are trimmed randomly. In the figure you can see three reads...
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Forum: Bioinformatics
04-23-2013, 01:29 AM
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Replies: 2
Views: 1,488
problem with R2 reads from Miseq
Dear, I have a problem in Miseq data. I have paired 2x150bp reads. I have identified some false positive (repetitive in different samples) due to short mapped reads. In fastq files (both R1 and R2) I...
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Forum: Bioinformatics
03-12-2013, 12:43 AM
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Replies: 2
Views: 1,337
read different length in fastq
Dear,
I have performed two runs (targeted sequencing) on miseq using 2x150bp protocol. Unusually, I have obtained fastq containing reads of different length, that during alignment step cause...
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Forum: Sample Prep / Library Generation
02-01-2013, 07:08 AM
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Replies: 0
Views: 1,266
enrichment efficiency
Dear,
I have design two different panels for two different diseases. The dimension of the target regions are the same (about 1.9Mb), in the first I there are 100 genes (only the exons), while in the...
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Forum: Bioinformatics
01-28-2013, 08:43 AM
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Replies: 4
Views: 7,187
Thank you very much for your help! The program...
Thank you very much for your help! The program runs and I have generated the new fastq. The last question is: how can I know from MISEQ reporter when the requeue and the rerun of "data extraction"...
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Forum: Bioinformatics
01-28-2013, 06:45 AM
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Replies: 4
Views: 7,187
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Forum: Bioinformatics
01-28-2013, 05:21 AM
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Replies: 4
Views: 7,187
miseq undetermined fastq
Good morning, I have a problem with miseq run.
I have generated 500Mb of Undetermined_sequence.fastq.gz and a sample in the trio was empty.
How can I determine raw index sequences in Undetermined...
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Forum: Bioinformatics
07-25-2012, 12:11 AM
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Replies: 1
Views: 1,207
CASAVA library problem
Dear,
the installation of CASAVA1.8 with cmake is not trivial for me!
I download the tar file, and tried to install all by cmake. But I have a problem in define library @CASAVA_FULL_PERL_LIBDIR@...
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Forum: Bioinformatics
05-31-2012, 05:54 AM
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Replies: 5
Views: 4,196
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Forum: Bioinformatics
04-11-2012, 06:08 AM
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Replies: 3
Views: 5,323
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Forum: Bioinformatics
04-11-2012, 02:23 AM
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Replies: 3
Views: 5,323
cummeRbund installation
Hi,
I'm trying to install cummeRbund package for final analysis of cufflinks outputs.
In R,
>install.packages("cummeRbund", dependencies = TRUE)
the error is that
package 'cummeRbund' is not...
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Forum: Bioinformatics
04-11-2012, 12:24 AM
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Replies: 1
Views: 1,017
RNASeq
Dear,
anyone could help me to "understand" the outputs of cufflinks?
How can I use these data and FPKM values to extract the differential gene expression and the different abundance of isoforms?
...
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Forum: Bioinformatics
04-06-2012, 07:58 AM
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Replies: 34
Views: 10,266
CONTRA cnv targeted resequencing
Dear I'm trying to run CONTRA on my data (targeted resequencing) to detect CNV in exons. The program returns me this error:
Traceback (most recent call last):
File "contra.py", line 34, in...
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Forum: Bioinformatics
03-14-2012, 03:58 AM
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Replies: 14
Views: 5,722
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Forum: Bioinformatics
03-14-2012, 03:30 AM
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Replies: 3
Views: 1,352
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Forum: Bioinformatics
03-07-2012, 02:34 AM
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Replies: 14
Views: 5,722
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Forum: Bioinformatics
03-05-2012, 01:38 AM
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Replies: 14
Views: 5,722
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Forum: Bioinformatics
03-01-2012, 05:01 AM
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Replies: 14
Views: 5,722
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Forum: Bioinformatics
02-27-2012, 06:40 AM
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Replies: 14
Views: 5,722
Dear Neha, I run GATK to recalibrate score as:...
Dear Neha, I run GATK to recalibrate score as: (i'm using version 1.3-25-g32cdef9) (this way it's ok)
> java -jar GenomeAnalysisTK.jar -R hg19.fasta -I sample.bam.sorted.bam --knownSites:dbsnp,VCF...
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