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Search: Posts Made By: dovah
Forum: General 11-13-2016, 09:51 AM
Replies: 1
Views: 1,432
Posted By dovah
retrieve all mRNA sequences for Drosophila

Hi,

where can I retrieve the reference annotation (with ID) for D. melanogaster?

I assembled my RNA reads using Cufflinks, but now I need to perform tblastx of my RNA seq assembled data vs...
Forum: Bioinformatics 11-08-2016, 02:19 PM
Replies: 7
Views: 3,007
Posted By dovah
Yes, this is what I mean by "extended cigar". By...

Yes, this is what I mean by "extended cigar". By the way, I found a tool that can do that a posteriori, in case someone else is interested: SamFixCigar (http://github.com/lindenb/jvarkit )
Forum: Bioinformatics 11-06-2016, 02:45 AM
Replies: 1
Views: 1,800
Posted By dovah
extended cigar in gmap

Hi all,

I am aligning pacbio reads to a reference genome using gmap. Do you know how to output an extended CIGAR in output sam file from gmap v 2016.08.10?

My command is:
gmap -d gmapDB -D...
Forum: Bioinformatics 11-06-2016, 02:36 AM
Replies: 7
Views: 3,007
Posted By dovah
extended cigar in bwa-mem

Hi all,

I am aligning pacbio reads to a reference genome using bwa mem. Do you know how to output an extended CIGAR in output sam file from bwa v0.7.13?

My command is:
bwa mem -x pacbio...
Forum: Pacific Biosciences 09-27-2016, 01:45 AM
Replies: 1
Views: 1,894
Posted By dovah
unique isoform detection using IsoSeq

Hi all,

I launched Iso-Seq on my RNA data (D. melanogaster). My aim is to see how many isoforms per gene are there in my sample. I am following the tutorial on github...
Forum: RNA Sequencing 08-24-2016, 12:55 AM
Replies: 1
Views: 1,734
Posted By dovah
sam format: SEQ field

Hi

I have a question regarding SAM format. What does it represent the field $10 (SEQ)? Checking SAM format manual (https://samtools.github.io/hts-specs/SAMv1.pdf), if I get it right, SEQ is the...
Forum: Oxford Nanopore 08-15-2016, 06:01 AM
Replies: 5
Views: 3,342
Posted By dovah
Thanks for reply, @gringer. However, may I ask...

Thanks for reply, @gringer. However, may I ask you which criteria you use to say that you got best result from a given mapper? aka, what are the criteria? I can probably imagine you take into account...
Forum: Bioinformatics 08-07-2016, 02:00 AM
Replies: 4
Views: 2,787
Posted By dovah
oh thanks Brian. I was so worried :P

oh thanks Brian. I was so worried :P
Forum: Bioinformatics 08-05-2016, 01:03 PM
Replies: 4
Views: 2,787
Posted By dovah
Ha ok, so it should be fine. Have you ever used...

Ha ok, so it should be fine. Have you ever used Cufflinks on bam file generated by Hisat2 by the way? Because it is taking a huge lot of time. I can spot CPU usage (~99%) but no tmp files in the...
Forum: Bioinformatics 08-05-2016, 05:20 AM
Replies: 4
Views: 2,787
Posted By dovah
XS tags in hisat2 alignment

Hi,

I had some troubles running Cufflinks with input mapping from HIsat2 (sam/bam).

Cufflinks man page (http://http://cole-trapnell-lab.github.io/cufflinks/cufflinks/index.html) says that...
Forum: Pacific Biosciences 08-03-2016, 10:56 PM
Replies: 3
Views: 1,757
Posted By dovah
RSII mapper benchmarking

Hi all,

I have RNA sequencing data (D. melanogaster) from 3 libraries (1-2Kb, 2-3Kb, 3-7Kb). What would be your suggestion for a mapper? I'm mostly interested in benchmarking isoform detection...
Forum: Oxford Nanopore 08-03-2016, 10:51 PM
Replies: 5
Views: 3,342
Posted By dovah
ONT MinION mapper benchmarking

Hi all,

I have RNA sequencing data (D. melanogaster) from r7 and r9 flowcells. What would be your suggestion for a mapper? I'm mostly interested in benchmarking isoform detection compared to...
Forum: RNA Sequencing 08-03-2016, 09:05 AM
Replies: 3
Views: 2,080
Posted By dovah
Hi! In my experience, using trimmomatic,...

Hi!

In my experience, using trimmomatic, you can use the information about your platform to remove universal adapters from your reads, no need to know the exact index sequence.

You can find...
Forum: RNA Sequencing 08-03-2016, 07:31 AM
Replies: 5
Views: 4,752
Posted By dovah
Hi again. Just for the sake of...

Hi again.

Just for the sake of completeness, and sharing:
* I generated sam file (almost 200GB) with Hisat2 with the option you suggested (--dta-cufflinks), to prepare XS flags for Cufflinks. ...
Forum: RNA Sequencing 08-02-2016, 06:13 AM
Replies: 5
Views: 4,752
Posted By dovah
Hi asier, many thanks for your answer. I...

Hi asier,

many thanks for your answer. I will try again the default samtools sort option, will let you know.

To answer your questions:
* The organism is D. melanogaster
* My bam files are...
Forum: RNA Sequencing 07-30-2016, 02:48 AM
Replies: 5
Views: 4,752
Posted By dovah
cufflinks: input alignment from hisat2

Hi all,

I read on Cufflinks (cole-trapnell-lab.github.io/cufflinks/cufflinks/index.html) man page that input bam file must be sorted this way:

sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted
...
Forum: RNA Sequencing 06-20-2016, 06:42 AM
Replies: 1
Views: 1,613
Posted By dovah
bioinformatics tool for RNA-seq data analysis: ideas wanted

Hi all :)

I'm planning to design a software tool for a bioinformatics programming project at university. It is mostly for fun during summer, but better if the software is useful and reusable for...
Forum: Bioinformatics 07-31-2014, 04:36 AM
Replies: 0
Views: 1,026
Posted By dovah
Parsing position in a protein sequence using perl

Hi!

I'd like to ask for help because I'm trying to deduce the relative positions in an ungapped sequence given the positions in a gapped sequence (from a multiple sequence alignment).
In order...
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