SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 19 of 19
Search took 0.02 seconds.
Search: Posts Made By: paulorapazote
Forum: Bioinformatics 06-10-2015, 02:40 AM
Replies: 33
Views: 11,291
Posted By paulorapazote
Sorry, I never worked with the command line. I...

Sorry, I never worked with the command line. I briefly checked the 2.2 version and command is

./astalavista.sh -c asta -i <input GTF> -o <output file>
Forum: Bioinformatics 06-09-2015, 08:25 AM
Replies: 33
Views: 11,291
Posted By paulorapazote
Astalavista

Hi,

Why dont you use the online version

http://genome.crg.es/astalavista/
Forum: Bioinformatics 12-04-2014, 07:11 AM
Replies: 3
Views: 2,729
Posted By paulorapazote
http://genome.crg.es/astalavista/

http://genome.crg.es/astalavista/
Forum: Bioinformatics 11-11-2014, 02:04 AM
Replies: 33
Views: 11,291
Posted By paulorapazote
Astalavista - too many intron retention events

Hi
Im running Astalavista and apparently the number of intron retention events reported is not accurate, in some cases the same event is counted more than once.
Astalavista predicts alternative...
Forum: RNA Sequencing 03-20-2014, 02:34 AM
Replies: 2
Views: 2,544
Posted By paulorapazote
Singletons

Hi

I have the same question. Apparently no, singletons are not used in the FPKM calculations. I found that in this link:


http://www.arrayserver.com/wiki/index.php?title=FPKM_Transcript
Forum: RNA Sequencing 02-18-2014, 07:31 AM
Replies: 12
Views: 5,432
Posted By paulorapazote
Hi again, I believe I understood why the...

Hi again,

I believe I understood why the number of genes reported is different at Cufflinks and Cuffmerge/Cuffdiff level.

I found that in many loci there are very few reads aligned (one, two)...
Forum: RNA Sequencing 11-21-2013, 07:48 AM
Replies: 12
Views: 5,432
Posted By paulorapazote
Hi I decided to investigate genes that could...

Hi

I decided to investigate genes that could be repeated (more than one gene exactly in the same locus) in the Cuffdiff output and I found around 2000 genes in these circumstances. Most of cases...
Forum: RNA Sequencing 11-11-2013, 03:17 AM
Replies: 12
Views: 5,432
Posted By paulorapazote
Hi Intermediate/comfortable experience in...

Hi

Intermediate/comfortable experience in Linux and TopHat (Tophat, Mapsplice, SpliceMap, Supersplat, Bowtie) beginner in Cufflinks (started 3 months ago).

Regards,

P
Forum: RNA Sequencing 11-11-2013, 01:27 AM
Replies: 12
Views: 5,432
Posted By paulorapazote
Diplication of genes Cufflinks/Cuffmerge

Thanks for your time.

I didnt find duplication of genes until now, but I am going to check with more detail.

I dont know why but the column with the coverage is normally empty in all files,...
Forum: RNA Sequencing 10-29-2013, 03:57 AM
Replies: 12
Views: 5,432
Posted By paulorapazote
I am performing differential analysis with 15...

I am performing differential analysis with 15 samples times 3 replicates, 45 in total.
When I run Cufflinks to assembly the genes/transcripts, I have 45 inputs and 45 outputs , right? At this stage...
Forum: RNA Sequencing 10-28-2013, 08:39 AM
Replies: 12
Views: 5,432
Posted By paulorapazote
Cufflinks/Cuffmerge pipeline

I am running the TopHat/Cufflinks/Cuffmerge/Cuffdiff pipeline in 45 samples (the specie is a plant), I dont have annotation, RNA-Seq analysis (Illumina 2x100bp reads).

I dont understand the...
Forum: Bioinformatics 07-23-2013, 06:55 AM
Replies: 11
Views: 26,577
Posted By paulorapazote
samtools flagstat output explanation

Hi

I am trying to find a detailed explanation to the samtools flagstat output, without success. Even in http://samtools.sourceforge.net/ there is no mention to the flagstat command...

Any...
Forum: Bioinformatics 07-18-2013, 02:58 AM
Replies: 6
Views: 5,431
Posted By paulorapazote
Threads problem??

Hi

I had similar problem, but strangely (TopHat version 2.0.7) the error message only occurred when running the job in a node with 4 cores ( -p 4 --num-threads option), and never with 16 cores...
Forum: Bioinformatics 07-06-2012, 01:18 AM
Replies: 2
Views: 1,959
Posted By paulorapazote
Hi Problem solved. I forgot to put the path...

Hi

Problem solved. I forgot to put the path of the read_end2:

I put "path/read_end1, read_end2" but the correct is "path/read_end1, path/read_end2".

Many thanks,

P
Forum: Bioinformatics 06-21-2012, 07:29 AM
Replies: 2
Views: 1,959
Posted By paulorapazote
MapSplice V1.15.2 error

Hi all

Im using Mapsplice with pair reads. I got the error message:


error: open entended file error

[FAILED]

Error: check reads format failed
Forum: RNA Sequencing 06-14-2012, 01:48 AM
Replies: 0
Views: 1,283
Posted By paulorapazote
SpliceMap gene annotation files

Hi

I'm trying to find the gene annotation file ( all.gene.refFlat.txt - gene annotation from Ensembl, RefSeq and knowngene ) to find novel junctions in SpliceMap.
Anyone knows where I can find...
Forum: RNA Sequencing 06-14-2012, 01:15 AM
Replies: 2
Views: 1,875
Posted By paulorapazote
Hi The Bowtie index problem could be related...

Hi

The Bowtie index problem could be related with the header of reference genome file - the empty spaces. Try to put only ">Chromosome1" (if you are working in fasta format) or delete the empty...
Forum: Bioinformatics 06-11-2012, 04:49 AM
Replies: 3
Views: 2,843
Posted By paulorapazote
Hi everyone I'm working with SuperSplat, and I...

Hi everyone
I'm working with SuperSplat, and I want to convert the final output (.supersplat) to Sam tools format? Any idea how can I do that?

Cheers,

P
Forum: Bioinformatics 05-09-2012, 01:26 AM
Replies: 0
Views: 845
Posted By paulorapazote
SuperSplat

HI. Apparently SuperSplat (Rna aligner) is not online anymore. Anyone knows why? :confused:
Showing results 1 to 19 of 19

 


All times are GMT -8. The time now is 02:33 AM.


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