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Forum: Bioinformatics 06-22-2017, 10:41 PM
Replies: 0
Views: 960
Posted By dekontrol
HISAT2: advantages of build index using annotated transcripts

Hello,

after reading the paper, I am still not sure about what is the advantage of building an index for HISAT2 by calling hisat2-build with options —s and —exon instead of using the genome...
Forum: Bioinformatics 05-24-2016, 08:31 AM
Replies: 5
Views: 1,938
Posted By dekontrol
Same problem. Moreover, Raw Map Mass becomes very...

Same problem. Moreover, Raw Map Mass becomes very very little respect to Normalized Map Mass. Does anybody found a solution?

Thanks
Forum: Bioinformatics 09-18-2015, 02:27 AM
Replies: 8
Views: 1,893
Posted By dekontrol
They told me that they think that they can make...

They told me that they think that they can make only one input from the same cell type, and use it as a reference input for all the future experiments from the same cell type..
Forum: Bioinformatics 09-18-2015, 02:17 AM
Replies: 8
Views: 1,893
Posted By dekontrol
Yes SylvainL, I am exacly in that situation: my...

Yes SylvainL, I am exacly in that situation: my wets wanted to use their old data.

Is there any paper that I can give to my wets, where is clearly stated that treatment and input should comes...
Forum: Bioinformatics 09-16-2015, 06:30 AM
Replies: 8
Views: 1,893
Posted By dekontrol
In the real world, sometimes you have to use old...

In the real world, sometimes you have to use old data with new data, or data that comes from different labs.. any idea?
Forum: Bioinformatics 09-16-2015, 06:14 AM
Replies: 8
Views: 1,893
Posted By dekontrol
MACS: ChIP and control with different tag size

Hi,
I am using MACS2 for ChIP-seq peak calling.

I have a treatment file with original reads of 51bp. Before alignment, the reads were dynamically trimmed on 3'end for removing low quality bases...
Forum: RNA Sequencing 10-06-2012, 11:22 PM
Replies: 2
Views: 1,589
Posted By dekontrol
I am using an aligner which don't have this...

I am using an aligner which don't have this option..(novoalign).. However if this is essential I can try other aligners like TopHat..
Forum: RNA Sequencing 10-02-2012, 06:12 AM
Replies: 2
Views: 1,589
Posted By dekontrol
Paired-end strand specific RNA-seq

Hi all,

I have aligned paired-end RNA-Seq data generated with a strand-specific library (on Illumina HiSeq).

Is possible to known how to assign the pairs to the RNA strand from which was...
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