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Forum: Bioinformatics 03-10-2015, 01:02 PM
Replies: 2
Views: 838
Posted By meher
Variable Insert sizes in targeted sequencing data

Hi,

We have targeted DNA-seq data for 30 samples. As part of the analysis we have calculated the insert size distributions in two scenarios:

1. Using all the aligned reads

2. Using all the...
Forum: Bioinformatics 08-18-2014, 05:54 AM
Replies: 0
Views: 1,242
Posted By meher
plink to VCF error

Hello all,


I have a ped and map file which are to be converted to vcf format.

A few genotypes from the ped file.

Sample1 Sample1 0 0 2 1 0 0 G G G G 0 0 C C G G G G A A T T
Sample2...
Forum: Bioinformatics 08-13-2014, 12:59 AM
Replies: 0
Views: 1,396
Posted By meher
Plink to VCF error

Hello all,


I have a ped and map file which are to be converted to vcf format.

A few genotypes from the ped file.

Sample1 Sample1 0 0 2 1 0 0 G G G G 0 0 C C ...
Forum: Bioinformatics 08-05-2014, 01:05 AM
Replies: 0
Views: 1,450
Posted By meher
Create VCF file from .bim, .fam and .bed files

Hi all,

I have a set of files: .bim, .fam and .bed files which has markers information for few individuals. I would need to convert these into a VCF format file. Could someone give...
Forum: Bioinformatics 03-27-2014, 09:16 AM
Replies: 3
Views: 1,014
Posted By meher
Yes, the data is from Genotyping arrays i.e....

Yes, the data is from Genotyping arrays i.e. Affymetrix genotyping arrays and Illumina genotyping arrays.
Forum: Bioinformatics 03-27-2014, 08:08 AM
Replies: 3
Views: 1,014
Posted By meher
Comparision of CNVs from Two different platfroms

Hi,

I am quiet new to CNV analysis and i have a general query.

I have SNP array data from Affymetrix and Illumina, would you please comment (or provide a reference) on the pros and cons of...
Forum: Bioinformatics 03-09-2014, 10:48 AM
Replies: 1
Views: 825
Posted By meher
Gene association to Phenotype

Hi all,

We have performed CNV study specific to a phenotype in humans and performed some bioinformatic analysis to prioritize the genes and picked up a gene based on the biological processes and...
Forum: Bioinformatics 11-15-2013, 03:02 AM
Replies: 17
Views: 9,183
Posted By meher
Thank you. As i thought both have the same...

Thank you. As i thought both have the same notation i.e. chr1,chr2.. they are in sync with each other but that seems to be costly.
Forum: Bioinformatics 11-15-2013, 01:57 AM
Replies: 17
Views: 9,183
Posted By meher
Here are the first few lines of sam file: ...

Here are the first few lines of sam file:

@HD VN:1.0 SO:coordinate
@SQ SN:gi|17737322|ref|chrMT| LN:16727
@SQ SN:gi|357579592|ref|chrX| LN:123869142
@SQ SN:gi|357579593|ref|chr38| LN:23914537...
Forum: Bioinformatics 11-14-2013, 09:51 AM
Replies: 17
Views: 9,183
Posted By meher
There are a few mapping to the features in gff...

There are a few mapping to the features in gff file. It is weird and no clue.
Forum: Bioinformatics 11-14-2013, 09:41 AM
Replies: 17
Views: 9,183
Posted By meher
I have done what u have suggested: ...

I have done what u have suggested:

htseq-count -i gene mini.sam gff3 -o mini_annot.sam

So what should be observed from mini_annot.sam?

$ wc -l mini.sam
10000 mini.sam
$ wc -l...
Forum: Bioinformatics 11-14-2013, 08:40 AM
Replies: 17
Views: 9,183
Posted By meher
Do you mean "NH:i:1"? because "NH:i:0" seems to...

Do you mean "NH:i:1"? because "NH:i:0" seems to be absent when it tried

samtools view -S accepted_hits.sam | grep "NH:i:0".
Forum: Bioinformatics 11-14-2013, 05:50 AM
Replies: 17
Views: 9,183
Posted By meher
I have placed semicolon before gene_id and tried...

I have placed semicolon before gene_id and tried htseq-count.

Error occured in line 6 of file ../refGene_canFam3.gff.
Error: need more than 1 value to unpack
[Exception type: ValueError, raised...
Forum: Bioinformatics 11-12-2013, 01:59 PM
Replies: 17
Views: 9,183
Posted By meher
I have tried using: htseq-count -i gene...

I have tried using:
htseq-count -i gene file.sam file.gff > count.txt

It processed without any error but the counts are zero.The output looks like:

A1BG 0
A1CF 0
A2M 0
A2ML1 0
.
Forum: Bioinformatics 11-12-2013, 11:53 AM
Replies: 17
Views: 9,183
Posted By meher
Could you give a sample output line of the gff...

Could you give a sample output line of the gff file showing how it should be modified?

Thanks.
Forum: Bioinformatics 11-12-2013, 11:28 AM
Replies: 17
Views: 9,183
Posted By meher
HTSeq 'gene_id' attribute error

I have just started using HTSeq and found problems using GFF file. I have checked some of the threads in seqanswers but couldn't fix.

Here is the command and error:

htseq-count sorted.sam...
Forum: Bioinformatics 10-23-2013, 05:13 AM
Replies: 0
Views: 1,548
Posted By meher
Multi-sample vs Single sample SNP calling for Linkage analysis

Hi,

We have performed SNP calling for 8 individuals with multi-sample approach and also individual SNP calling using GATK. Below are the few output lines from the outputs.

Multisample SNP...
Forum: Bioinformatics 10-12-2013, 07:02 AM
Replies: 10
Views: 5,513
Posted By meher
Here are the few lines of the annotation file: ...

Here are the few lines of the annotation file:

chr1 14548 BICF2G630707759 0
chr1 80040 BICF2P1173580 0
chr1 82626 BICF2G630707846 0
chr1 212740 BICF2P1383091 0

And the vcf file is generated...
Forum: Bioinformatics 10-11-2013, 10:22 PM
Replies: 10
Views: 5,513
Posted By meher
Okay. But, i have to mention that my genome is...

Okay. But, i have to mention that my genome is not human. The annotation file is the genotyped positions for the dog genome and the format is as shown in the previous post.

So, what is meant my...
Forum: Bioinformatics 10-11-2013, 04:31 AM
Replies: 10
Views: 5,513
Posted By meher
Thanks for the suggestion. I have checked the...

Thanks for the suggestion. I have checked the tool LINKDATAGEN and tried to convert the vcf to merlin input format. But, here is an error which i met with the first step:

vcf2linkdatagen.pl...
Forum: Bioinformatics 10-09-2013, 06:40 AM
Replies: 10
Views: 5,513
Posted By meher
Linkage analysis for WGS data

Hi all,

We have performed whole genome sequencing(WGS) in 6 affected individuals and 2 parent samples to identify the causal variant for a particular phenotype. The disease is known to inherit by...
Forum: Bioinformatics 06-26-2013, 03:31 AM
Replies: 8
Views: 3,251
Posted By meher
Thanks it worked. But could it be possible to...

Thanks it worked. But could it be possible to find, how much percentage of the exons are covered by atleast 1X/5X/10X reads out of the coverageBed output?
Forum: Bioinformatics 06-25-2013, 10:48 AM
Replies: 8
Views: 3,251
Posted By meher
Okay. But there are seven columns in the output....

Okay. But there are seven columns in the output. First three gives the chromosome number, start and end position. The next two columns are zero's and sixth is the length of the exon and the last is...
Forum: Bioinformatics 06-25-2013, 10:01 AM
Replies: 8
Views: 3,251
Posted By meher
Sorry that i couldn't understand, what do you...

Sorry that i couldn't understand, what do you mean by default output? Is it from

samtools view -b <BAM> | coverageBed -abam stdin -b exons.bed

or

samtools view -b | coverageBed -abam stdin...
Forum: Bioinformatics 06-25-2013, 09:52 AM
Replies: 8
Views: 3,251
Posted By meher
Can we get a single value like x% of exons are...

Can we get a single value like x% of exons are covered from the output?
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