SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 15 of 15
Search took 0.04 seconds.
Search: Posts Made By: a.kmg
Forum: Bioinformatics 08-26-2015, 06:11 AM
Replies: 0
Views: 707
Posted By a.kmg
Forum: Bioinformatics 02-26-2015, 03:52 AM
Replies: 3
Views: 1,702
Posted By a.kmg
Hi, Thank you for your different ideas. ...

Hi,

Thank you for your different ideas.

I used R to do that:

I imported my .gtf annotation file from ensembl:


My original GTF file contained 57,773 annotated genes.
Forum: Bioinformatics 02-20-2015, 07:11 AM
Replies: 3
Views: 1,702
Posted By a.kmg
How to determine the proportion of overlapping genes in a genome?

Hello to all,

I'm working on stranded RNA-seq data and I would justify the use of this type of protocol, showing the proportion of genes that overlapp on the genome (human). Indeed, thanks to...
Forum: Bioinformatics 02-20-2015, 07:07 AM
Replies: 3
Views: 1,382
Posted By a.kmg
Thank you dpryan. I currently testing...

Thank you dpryan.

I currently testing Rcount, a new tool where alignments of multireads are weighted based on the number of uniquely aligned reads in the neighborhood.

And I tested...
Forum: Bioinformatics 01-27-2015, 12:44 AM
Replies: 3
Views: 1,382
Posted By a.kmg
A great tool to count multiple aligned reads.

Dear members of seqanswers,

Do you know a tool for counting multiple aligned reads?

Currently I use the htseq-count tool, but it doesn't take into account this type of read.

I know...
Forum: Bioinformatics 12-19-2014, 03:46 AM
Replies: 3
Views: 2,245
Posted By a.kmg
I write here the solution of my problem. ...

I write here the solution of my problem.

Some of my files have been corrupted during the transfer of these files from sequencer to my server.

To ignore this corrupted files, the tech support of...
Forum: Bioinformatics 12-17-2014, 06:53 AM
Replies: 3
Views: 2,245
Posted By a.kmg
Thank you for your reply. Yes I can read...

Thank you for your reply.

Yes I can read this file, the size is different of 0 and I tried with the --ignore-missing-bcl option but I get the same error ... that's why I really do not understand...
Forum: Bioinformatics 12-17-2014, 06:38 AM
Replies: 3
Views: 2,245
Posted By a.kmg
bclToFastq conversion error

Hello to all,

I get some errors with the bclToFastq tool, of type:




But when I do, for example:
Forum: Bioinformatics 12-02-2014, 01:08 AM
Replies: 0
Views: 1,057
Posted By a.kmg
RNA-seq - Recovering antisense RNA counts

Hello to all,

I have RNA-seq data generated with the mRNA stranded protocol of Illumina (which is a dUTP protocol).

Generally, I used TopHat/Bowtie and htseq-count to align and quantify my...
Forum: Bioinformatics 09-24-2014, 05:57 AM
Replies: 0
Views: 1,497
Posted By a.kmg
Identifying antisense transcript with stranded mRNA-seq.

Hello to all,

I have one dataset that contains samples (2 conditions in 2 replicates) sequenced with "TruSeq Stranded mRNA Sample Prep Kit" : directional mRNA-seq.

How is it possible to study...
Forum: Bioinformatics 09-18-2014, 06:36 AM
Replies: 0
Views: 926
Posted By a.kmg
How to interpret "align_summary.txt" of TopHat2.

Hello,

I use TopHat2 to generate the alignment of my paired-end fastq files.

The following "align_summary.txt" is created :



how to determine the number of uniquely aligned reads ?
Forum: Bioinformatics 08-07-2014, 05:16 AM
Replies: 3
Views: 1,432
Posted By a.kmg
You're welcome :)

You're welcome :)
Forum: Bioinformatics 08-07-2014, 05:07 AM
Replies: 1
Views: 1,215
Posted By a.kmg
Reads coverage along genes in RNA-seq

Hello everyone,

In RNA-seq, it seems that the coverage of reads along the gene is not uniform.

Indeed, it is possible that reads covering is more high in 5', 3', ...

There is a way of...
Forum: Bioinformatics 08-07-2014, 03:29 AM
Replies: 7
Views: 2,095
Posted By a.kmg
You can run Bowtie2 with your fastq file on...

You can run Bowtie2 with your fastq file on E.coli to suppress reads corresponding to E.coli :



This command treats the raw fastq file, creating a new fastq containing not E.coli reads (--un =...
Forum: Bioinformatics 08-06-2014, 11:59 PM
Replies: 3
Views: 1,432
Posted By a.kmg
You can use the Biomart of Ensembl to recover...

You can use the Biomart of Ensembl to recover this file.

http://www.ensembl.org/biomart/

Choose your dataset (human, mouse, ...)

Select the attributes you want. Here:

Features => GENE :
Showing results 1 to 15 of 15

 


All times are GMT -8. The time now is 11:14 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO