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Forum: Bioinformatics 01-06-2015, 06:27 AM
Replies: 1
Views: 1,386
Posted By huma Asif
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...
Forum: Illumina/Solexa 12-09-2014, 04:49 AM
Replies: 4
Views: 2,746
Posted By huma Asif
thank you for your help i will try that

thank you for your help
i will try that
Forum: Illumina/Solexa 12-09-2014, 03:42 AM
Replies: 4
Views: 2,746
Posted By huma Asif
i corrected that but now getting this error ...

i corrected that but now getting this error
failed to open input file 'GO06_2500_Mate.read2.fastq': Value too large for defined data type
Forum: Illumina/Solexa 12-09-2014, 02:08 AM
Replies: 4
Views: 2,746
Posted By huma Asif
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...
Forum: Bioinformatics 12-08-2014, 04:52 AM
Replies: 0
Views: 941
Posted By huma Asif
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 ...
Forum: Bioinformatics 09-08-2014, 11:24 AM
Replies: 7
Views: 1,365
Posted By huma Asif
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...
Forum: Bioinformatics 09-08-2014, 11:19 AM
Replies: 9
Views: 3,697
Posted By huma Asif
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
Forum: Bioinformatics 09-08-2014, 11:12 AM
Replies: 7
Views: 1,365
Posted By huma Asif
GenoMax yes :)

GenoMax
yes :)
Forum: Bioinformatics 09-08-2014, 10:45 AM
Replies: 9
Views: 3,697
Posted By huma Asif
how i can convert >1...>2....>3...>10000 to >1...

how i can convert
>1...>2....>3...>10000 to >1

and
>1..>2..>3....>10000 for b.fasta to >2 and
same for for all my 5 samples
Forum: Bioinformatics 09-08-2014, 08:10 AM
Replies: 7
Views: 1,365
Posted By huma Asif
how i can convert >1...>2....>3...>10000 to >1...

how i can convert
>1...>2....>3...>10000 to >1

and
>1..>2..>3....>10000 for b.fasta to >2 and
same for for all my 5 samples
i have to use this file for multiple alignment
Forum: Bioinformatics 09-08-2014, 07:34 AM
Replies: 7
Views: 1,365
Posted By huma Asif
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...
Forum: Bioinformatics 09-05-2014, 09:03 AM
Replies: 8
Views: 2,179
Posted By huma Asif
tried with small l still n in final output please...

tried with small l still n in final output please suggest where i can get wrong

see my code
samtools mpileup -uf human_hg19.fa reads.bam -l targetSeq_exome_target_regions_hg19.bed |bcftools view...
Forum: Bioinformatics 09-05-2014, 07:25 AM
Replies: 8
Views: 2,179
Posted By huma Asif
thank you so much i am going to try this now

thank you so much i am going to try this now
Forum: Bioinformatics 09-05-2014, 06:14 AM
Replies: 8
Views: 2,179
Posted By huma Asif
give the same result with -L see my code ...

give the same result with -L

see my code
samtools mpileup -uf human_hg19.fa reads.bam -L targetSeq_exome_target_regions_hg19.bed |bcftools view -cg -...
Forum: Bioinformatics 09-04-2014, 12:09 PM
Replies: 8
Views: 2,179
Posted By huma Asif
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...
Forum: Bioinformatics 09-04-2014, 07:57 AM
Replies: 8
Views: 2,179
Posted By huma Asif
thank you so much will try now :)

thank you so much will try now :)
Forum: Bioinformatics 09-04-2014, 07:32 AM
Replies: 8
Views: 2,179
Posted By huma Asif
consensus fasta and multifasta file of human genomes

Dear All,
i desperately need help in converting a thought to work.

i have sequence six human samples and have created six alignment file (BAM) using UCSC reference.
i need to do multiple...
Forum: Bioinformatics 08-28-2014, 06:41 AM
Replies: 1
Views: 967
Posted By huma Asif
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...
Forum: Bioinformatics 08-18-2014, 09:55 AM
Replies: 0
Views: 1,132
Posted By huma Asif
Vcf file filtering

need help in filtering population subset of variants from 1KGP vcf file
Forum: Bioinformatics 08-08-2014, 05:11 AM
Replies: 25
Views: 2,802
Posted By huma Asif
can you help me how i can get rid of 1,2,3, in...

can you help me how i can get rid of 1,2,3, in first column
> head(rawcounts)
Gene.ID A B
1 WASH7P 1 0
2 FAM138A 0 0
3 FAM138F 0 0
4 OR4F5 0 ...
Forum: Bioinformatics 08-07-2014, 02:04 PM
Replies: 25
Views: 2,802
Posted By huma Asif
thank you dpryan

thank you dpryan
Forum: Bioinformatics 08-07-2014, 07:43 AM
Replies: 25
Views: 2,802
Posted By huma Asif
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...
Forum: Bioinformatics 08-07-2014, 04:27 AM
Replies: 25
Views: 2,802
Posted By huma Asif
thank you i read all that but do i need to write...

thank you i read all that but do i need to write names of my count file or path where my files are my current diectory is where my gff and count files are
Forum: Bioinformatics 08-06-2014, 12:34 PM
Replies: 25
Views: 2,802
Posted By huma Asif
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,...
Forum: Bioinformatics 08-06-2014, 10:50 AM
Replies: 25
Views: 2,802
Posted By huma Asif
> ecs <- read.HTSeqCounts( +...

> ecs <- read.HTSeqCounts(
+ sampleTable$countFile,
+ sampleTable,
+ flattenedfile="gene.gff")
Error in checkAtAssignment("character", "annotationFile", "character") :
‘annotationFile’ is...
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