Forum: Bioinformatics
01-06-2015, 07:27 AM
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Replies: 1
Views: 1,506
vcf_to_ped_convert.pl
Dear All,
i need your help in visualizing 1000 genome data in haploview
when I upload the file on Haploview version 4.2 i get this error
more than two alleles at marker 300
Any help would be...
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Forum: Illumina/Solexa
12-09-2014, 05:49 AM
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Replies: 4
Views: 2,984
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Forum: Illumina/Solexa
12-09-2014, 04:42 AM
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Replies: 4
Views: 2,984
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Forum: Illumina/Solexa
12-09-2014, 03:08 AM
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Replies: 4
Views: 2,984
FastX tool :: fastq_quality_filter
Dear All,
i am doing quality filtering of my fastq file using fastq_quality_filter
and i am getting this error
Premature End-Of-File (filename ='-')
my code is
nohup fastq_quality_filter ‐v...
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Forum: Bioinformatics
12-08-2014, 05:52 AM
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Replies: 0
Views: 1,082
SOLID & FastQC tool kit
Hello everyone,
I have SOLiD Mate pair data which I am trying to pass through QC checks. what i did so far
1) Convert XSQ to fastq (using XSQtools)
2)solid2fastq.pl from bwa
can i use this ...
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Forum: Bioinformatics
09-08-2014, 12:24 PM
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Replies: 7
Views: 1,516
i want all the genes e.g in sample 1 to be...
i want all the genes e.g in sample 1 to be concatenated as >1 likewise for my all samples
my thought is as all genes in all files are in same order so when i have multifasta as >1, >2, >3,>4,>5
i...
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Forum: Bioinformatics
09-08-2014, 12:19 PM
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Replies: 9
Views: 4,173
i created fasta from vcf file using target...
i created fasta from vcf file using target intervals so now in fasta file i have the same number of header as the coordinates in bed
so what i am doing is i want to cat all these sequences
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Forum: Bioinformatics
09-08-2014, 12:12 PM
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Replies: 7
Views: 1,516
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Forum: Bioinformatics
09-08-2014, 11:45 AM
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Replies: 9
Views: 4,173
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Forum: Bioinformatics
09-08-2014, 09:10 AM
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Replies: 7
Views: 1,516
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Forum: Bioinformatics
09-08-2014, 08:34 AM
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Replies: 7
Views: 1,516
MUltifasta file
hi every one,
what i need to do is i need multiple sequence alignment file
i converted the vcf file to consensus fasta and "cat" all these consensus sequence into multifasta.
in my...
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Forum: Bioinformatics
09-05-2014, 10:03 AM
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Replies: 8
Views: 2,552
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Forum: Bioinformatics
09-05-2014, 08:25 AM
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Replies: 8
Views: 2,552
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Forum: Bioinformatics
09-05-2014, 07:14 AM
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Replies: 8
Views: 2,552
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Forum: Bioinformatics
09-04-2014, 01:09 PM
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Replies: 8
Views: 2,552
well i am done with first step but look at my...
well i am done with first step but look at my fastq file with many NNNNNNNNNN
is this because my data is targeted exome sequencing
how can i get rid of it
if i use this fastq in seqtk it gives...
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Forum: Bioinformatics
09-04-2014, 08:57 AM
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Replies: 8
Views: 2,552
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Forum: Bioinformatics
09-04-2014, 08:32 AM
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Replies: 8
Views: 2,552
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Forum: Bioinformatics
08-28-2014, 07:41 AM
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Replies: 1
Views: 1,118
continent-specific variants
Dear All,
Can any body help me in how can i extract continent specific variants from 1000 genome All population variant set
e.g i have downloaded 1000G_phase1.snps.high_confidence.hg19.vcf from...
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Forum: Bioinformatics
08-18-2014, 10:55 AM
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Replies: 0
Views: 1,273
Vcf file filtering
need help in filtering population subset of variants from 1KGP vcf file
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Forum: Bioinformatics
08-08-2014, 06:11 AM
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Replies: 25
Views: 3,199
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Forum: Bioinformatics
08-07-2014, 03:04 PM
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Replies: 25
Views: 3,199
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Forum: Bioinformatics
08-07-2014, 08:43 AM
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Replies: 25
Views: 3,199
while its going let me explain you a problem...
while its going let me explain you a problem about DESeq
i tried to use input file with genenames but it was giving me this error
Error in round(countData) : non-numeric argument to mathematical...
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Forum: Bioinformatics
08-07-2014, 05:27 AM
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Replies: 25
Views: 3,199
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Forum: Bioinformatics
08-06-2014, 01:34 PM
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Replies: 25
Views: 3,199
please help me in creating
DEXSeqDataSet
i...
please help me in creating
DEXSeqDataSet
i am confused what shall i give in place of countFiles
where do i specify my files in this code
dxd = DEXSeqDataSetFromHTSeq(
countFiles,...
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Forum: Bioinformatics
08-06-2014, 11:50 AM
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Replies: 25
Views: 3,199
> ecs <- read.HTSeqCounts(
+...
> ecs <- read.HTSeqCounts(
+ sampleTable$countFile,
+ sampleTable,
+ flattenedfile="gene.gff")
Error in checkAtAssignment("character", "annotationFile", "character") :
‘annotationFile’ is...
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