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Forum: Bioinformatics 06-24-2013, 09:29 AM
Replies: 1
Views: 3,759
Posted By alpesh
detecting predominant exons using DEXSeq, edgeR

Hi all,

I have RNA-seq data for 3 conditions (with biological replicates), and I`m hoping to investigate how the exon usage varies across conditions. I am using testGeneForDEU and spliceVariants...
Forum: Bioinformatics 06-18-2013, 03:20 PM
Replies: 6
Views: 1,661
Posted By alpesh
let me give an example. A couple of lines...

let me give an example.

A couple of lines from my gtf file shows coordinates of a gene and its first exon

chr1 dexseq_prepare_annotation.py aggregate_gene 300422454 300435350 . + . gene_id...
Forum: Bioinformatics 06-18-2013, 01:43 PM
Replies: 6
Views: 1,661
Posted By alpesh
hi dpryan, i have to use AGPv2.62 ...

hi dpryan, i have to use AGPv2.62 annotation,,,the my gtf file has chr1,chr2 etc., when you say none of the reads are paired end, it is because of the column 2 flags being 16 (reverse strand),...
Forum: Bioinformatics 06-18-2013, 12:14 PM
Replies: 6
Views: 1,661
Posted By alpesh
python dexseq_count.py zea_mays.AGPv2.62.gff...

python dexseq_count.py zea_mays.AGPv2.62.gff sorted_samfile.sam exon_counts.txt

Here is the command I used, all the exons (for 30k genes) come up with a 0 number in the output if nothing is...
Forum: Bioinformatics 06-18-2013, 11:07 AM
Replies: 6
Views: 1,661
Posted By alpesh
getting dexseq_count.py to work

Hi,

Can you help me in this? I have paired end reads in sam format, and I have followed all steps to create the sorted sam file according to the passilla tutorial. I have successfully created the...
Forum: Bioinformatics 10-12-2011, 12:38 PM
Replies: 1
Views: 9,865
Posted By alpesh
Extracting reads from BAM files

Hi All,

I am new to samtools and some help will be awesome.

I have BAM files and I have a long list of loci which I want to extract reads for. Basically I want to pass a lot a loci in the...
Forum: Bioinformatics 10-12-2011, 12:33 PM
Replies: 4
Views: 6,131
Posted By alpesh
A region can be presented, for example, in the...

A region can be presented, for example, in the following format: ‘chr2’ (the whole chr2), ‘chr2:1000000’ (region starting from 1,000,000bp) or ‘chr2:1,000,000-2,000,000’ (region between 1,000,000 and...
Showing results 1 to 7 of 7

 


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