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Search: Posts Made By: tir_al
Forum: Bioinformatics 07-20-2013, 02:55 AM
Replies: 5
Views: 2,461
Posted By tir_al
Dear Helical, It seem I have bumped into...

Dear Helical,

It seem I have bumped into the same problem that is troubling you - cufflinks recognizes paired reads as single end ones.
Did you manage to solve your problem?

My best guess is...
Forum: General 01-10-2013, 05:50 AM
Replies: 16
Views: 11,030
Posted By tir_al
I currently have no options, and no place for new...

I currently have no options, and no place for new disk space :)
Forum: General 01-09-2013, 03:25 PM
Replies: 16
Views: 11,030
Posted By tir_al
Yeah. Preferably for storing old projects.

Yeah. Preferably for storing old projects.
Forum: General 01-09-2013, 01:26 PM
Replies: 16
Views: 11,030
Posted By tir_al
I tried it on 75bp, cca 80 mil. reads, pair end...

I tried it on 75bp, cca 80 mil. reads, pair end bam file. And it crammed 3.6 GB file into a 257MB archive.
Forum: General 01-09-2013, 07:34 AM
Replies: 16
Views: 11,030
Posted By tir_al
Tnx for the prompt answer! I just tried cram...

Tnx for the prompt answer!

I just tried cram today. The compression ratio is extremely impressive, but it's a too slow for my needs.
Forum: General 01-09-2013, 07:05 AM
Replies: 16
Views: 11,030
Posted By tir_al
FastQ/BAM compression

Does anybody know of a more recent comparison of algorithms for fastq/bam compression, than this thread?
http://seqanswers.com/forums/showthread.php?t=6349

Best
Forum: Literature Watch 12-11-2012, 05:55 AM
Replies: 1
Views: 1,260
Posted By tir_al
You might check this paper pmid:21854988 ...

You might check this paper pmid:21854988

Best
Forum: RNA Sequencing 11-15-2012, 02:20 AM
Replies: 16
Views: 18,688
Posted By tir_al
Dear Devkin, The heatmap you posted was...

Dear Devkin,

The heatmap you posted was done in R using the ggplot2 package.

As you are already using the tuxedo pipeline, you could take a look at the cummeRbund...
Forum: Bioinformatics 09-11-2012, 04:44 AM
Replies: 0
Views: 919
Posted By tir_al
Mapping to colorspace genomes

I tried playing around with mapping of SOLID reads in colorspace and letterspace, and the two do not look even slightly alike.

The mapping to color space has much more reads that map to multiple...
Forum: Bioinformatics 07-19-2012, 04:21 AM
Replies: 1
Views: 1,330
Posted By tir_al
Have you tried checking papers from the Fantom...

Have you tried checking papers from the Fantom consortium?

They deal primarily with CAGE data and have developed algorithms for TSS finding and annotation.

If you pubmed Carnici P., you can...
Forum: Bioinformatics 07-18-2012, 12:42 PM
Replies: 0
Views: 1,056
Posted By tir_al
Bowtie and NH tag

How do you get bowtie to but the NH tags when the reads are multimapped?
Forum: Bioinformatics 07-04-2012, 07:11 AM
Replies: 3
Views: 1,025
Posted By tir_al
I somehow doubt that the NPS will give you the...

I somehow doubt that the NPS will give you the results you want. I tried doing the nucleosome prediction on my H3k4me3 and H2A.z sonicated samples, and the results were almost random. If you really...
Forum: Bioinformatics 07-02-2012, 04:40 PM
Replies: 3
Views: 1,025
Posted By tir_al
Is your data MNase digested or fragmented by...

Is your data MNase digested or fragmented by sonication?

I know that if you have H3k4me3 MNase seq, the position of individual nucleosomes can be visualized, but with sonication you just get a...
Forum: Bioinformatics 04-11-2012, 05:12 AM
Replies: 9
Views: 9,388
Posted By tir_al
If you want to do genome wide correlation in R,...

If you want to do genome wide correlation in R, you will need 2 bioconductor packages: RSamtools and GenomicRanges, and also the lengths for the chromosomes from the corresponding genome.

The...
Forum: Illumina/Solexa 02-24-2012, 02:12 AM
Replies: 5
Views: 6,582
Posted By tir_al
You can also dowload it fro ENA: ...

You can also dowload it fro ENA:
http://www.ebi.ac.uk/ena/data/view/SRP007412

They have a nice .tsv description file of the whole experiment, which can be used to automate the download.
Forum: Bioinformatics 02-24-2012, 02:09 AM
Replies: 16
Views: 20,237
Posted By tir_al
If you run FastQC...

If you run FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/), it will tell you whether some of the overrepresented sequences in the sample correspond to known illumina adapters.
Forum: Bioinformatics 01-26-2012, 04:27 AM
Replies: 1
Views: 2,401
Posted By tir_al
You could try Seqmonk...

You could try Seqmonk (http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/)
Forum: Bioinformatics 12-09-2011, 02:06 AM
Replies: 1
Views: 1,040
Posted By tir_al
In Bioconductor the most highly used packages are...

In Bioconductor the most highly used packages are DESeq and EdgeR.
Forum: General 09-01-2011, 02:01 AM
Replies: 2
Views: 1,602
Posted By tir_al
I tried it also. For genes with decent coverage...

I tried it also. For genes with decent coverage it worked extremely well.
Forum: De novo discovery 06-22-2011, 03:18 AM
Replies: 2
Views: 2,115
Posted By tir_al
You could try the "Trinity pipeline". It does...

You could try the "Trinity pipeline". It does transcriptome reconstruction without the reference genome.

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.1883.html

Best regards.
Forum: Bioinformatics 04-06-2011, 03:18 AM
Replies: 1
Views: 2,671
Posted By tir_al
Have you tried looking at the duplication rate of...

Have you tried looking at the duplication rate of your libraries? Although the distributions might look the same in the browser, the high duplication rate in one sample can really mess up the peak...
Forum: Bioinformatics 01-21-2011, 10:25 AM
Replies: 66
Views: 28,490
Posted By tir_al
Cisgenome V2 Genome selection

Dear Hji,

Could you please tell me in which way to choose the appropriate genome for my samples in cisgeome v2 on linux os?

I couldn't find the flag in the seqpeak application.

Reagards.
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