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Search: Posts Made By: EGrassi
Forum: Service Providers 07-24-2013, 02:21 AM
Replies: 15
Views: 4,990
Posted By EGrassi
Oh, sure, reading a thread about companies me and...

Oh, sure, reading a thread about companies me and my smaller IQ will check the correspondences between user names - and given CEO e-mails when one says things like "they have good software..."....
Forum: Bioinformatics 06-20-2013, 05:08 AM
Replies: 0
Views: 1,414
Posted By EGrassi
tophat 2.0.0 and index fasta file

Hello, I was wondering, as long as I believe that bowtie only uses its indexes to perform
the alignments, what does tophat do with the reference fasta file referred here:
...
Forum: RNA Sequencing 05-31-2013, 01:41 AM
Replies: 15
Views: 9,271
Posted By EGrassi
From the manual: -g/--max-multihits <int>...

From the manual:
-g/--max-multihits <int> Instructs TopHat to allow up to this many alignments to the reference for a given read, and choose the alignments based on their alignment scores if there...
Forum: Bioinformatics 04-11-2013, 08:38 AM
Replies: 6
Views: 3,827
Posted By EGrassi
In theory a pipe avoids writing all the...

In theory a pipe avoids writing all the intermediate results to the disk thus is more efficient, sadly it is not always possible/easy to combine different tools with pipelines.
Forum: Bioinformatics 04-11-2013, 04:27 AM
Replies: 2
Views: 1,187
Posted By EGrassi
Wooops! I didn't notice the release date :)...

Wooops! I didn't notice the release date :) Thanks. I wrote to the SourceForge mailing list so hopefully a developer will notice it and fix the zip.

Thanks!
Forum: Bioinformatics 04-10-2013, 01:13 PM
Replies: 2
Views: 1,187
Posted By EGrassi
Compiling bowtie 1.0.0 from source

I feel stupid about this as long as I cannot believe that nobody has met this problem until now. I'm trying to compile bowtie 1.0.0 from source on a "vanilla linux" with gcc and I am encountering...
Forum: Bioinformatics 03-27-2013, 01:09 AM
Replies: 123
Views: 44,924
Posted By EGrassi
Thanks! Looking forward to the new options. ...

Thanks! Looking forward to the new options.

Is it just me or the bioconductor linked vignette is a 16Mb pdf with 10701 pages and a lot of repetitions starting from page 6?
Forum: Bioinformatics 01-16-2013, 07:21 AM
Replies: 9
Views: 1,575
Posted By EGrassi
or ls | xargs ...

or ls | xargs ...
Forum: Bioinformatics 01-16-2013, 03:04 AM
Replies: 11
Views: 2,091
Posted By EGrassi
I'm wondering why the join step is...

I'm wondering why the join step is needed...wouldn't grep -v -f file1 file2 be sufficient (as long as ID of different proteins than the one of a given line should not appear in file2, I think)?
Forum: Bioinformatics 01-15-2013, 11:30 PM
Replies: 3
Views: 982
Posted By EGrassi
As long as the samtools flagstat percentage of...

As long as the samtools flagstat percentage of properly paired reads gotten on the accepted_hits changed setting the -r tophat parameter I believed that the ones reported as not properly aligned were...
Forum: Bioinformatics 01-15-2013, 01:08 AM
Replies: 3
Views: 982
Posted By EGrassi
A quick check on the htseq_count code tells me...

A quick check on the htseq_count code tells me that it never uses the reads "mate_aligned" attribute and just considers all of the paired reads. Does this seem a strange behaviour only to me? I don't...
Forum: Bioinformatics 01-14-2013, 01:15 AM
Replies: 3
Views: 982
Posted By EGrassi
Tophat + htseq_count

Hello, I'm performing RNAseq analyses and I've stumbled upon some puzzling results.
I aligned some data with tophat2 (default settings) and as long as the results were disappointing (only about 5%...
Forum: Bioinformatics 01-14-2013, 12:00 AM
Replies: 4
Views: 1,361
Posted By EGrassi
What does samtools flagstat on the...

What does samtools flagstat on the accepted_hits.bam and rejected looks like?

Just to mention the fact: I had some paired data with fastqc results similar to yours and quality trimming lead me to...
Forum: Bioinformatics 11-28-2012, 05:48 AM
Replies: 44
Views: 30,059
Posted By EGrassi
Can I ask which options did you use for your...

Can I ask which options did you use for your tests of tophat-star? Some default values seems very different (for example about multi mapped reads) and I would like to avoid losing something...thank...
Forum: RNA Sequencing 11-08-2012, 10:55 PM
Replies: 8
Views: 7,730
Posted By EGrassi
This traceback seems to suggest a samtools...

This traceback seems to suggest a samtools related problem. I would suggest you to try to understand how samtools is invoked by tophat and try that by hand and check if all the related files are...
Forum: Bioinformatics 11-08-2012, 10:45 PM
Replies: 8
Views: 2,487
Posted By EGrassi
I saw BEER too but did not read the results (bad...

I saw BEER too but did not read the results (bad bad Elena!).
Thanks for the interesting post, right now I'm not directly interested in cufflinks alternate transcript capabilities but who know what...
Forum: Bioinformatics 11-08-2012, 10:39 PM
Replies: 8
Views: 2,487
Posted By EGrassi
First of all thank you for your help. I would...

First of all thank you for your help. I would like to add all the possible support to your rant, I'm worried that this is shoddy science also :(

I looked at those reads qualities with fastqc and...
Forum: Bioinformatics 11-07-2012, 11:49 PM
Replies: 8
Views: 2,487
Posted By EGrassi
I had to delete the tophat 2.0.0 result to avoid...

I had to delete the tophat 2.0.0 result to avoid filling our hd of data when doing "trial and error". Tophat 2.0.4 is telling:
prep_reads v2.0.4 (3480M)
---------------------------
204037 out of...
Forum: Bioinformatics 11-07-2012, 08:39 AM
Replies: 8
Views: 2,487
Posted By EGrassi
With tophat 2.0.4 the logs are similar but: $...

With tophat 2.0.4 the logs are similar but:
$ samtools flagstat accepted_hits.bam
10819957 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
10819957 + 0 mapped (100.00%:-nan%)...
Forum: Bioinformatics 11-02-2012, 08:07 AM
Replies: 8
Views: 2,487
Posted By EGrassi
Tophat 2.0.0 number of reads

Apart from the problem when using more than one core and random problems there I've got some other problems:

$ wc -l ../reads/SRR306839.fastq
75400120 ../reads/SRR306839.fastq

Thus I have...
Forum: Bioinformatics 10-11-2012, 01:01 AM
Replies: 6
Views: 1,093
Posted By EGrassi
...because of tophat?

Ok, as long as fastq seems fine to me (they have an id foreach read, for example) I'm starting to think that the strange bam/sam obtained are tophat's responsibility.

I have "normal" lines like...
Forum: Bioinformatics 10-10-2012, 05:36 AM
Replies: 6
Views: 1,093
Posted By EGrassi
Ok, I tried removing from the .sam files lines...

Ok, I tried removing from the .sam files lines with an empty read name (I hope to understand why they're there) and it finished without any problem, the counts seems sensible to me (not from a...
Forum: Bioinformatics 10-10-2012, 05:13 AM
Replies: 6
Views: 1,093
Posted By EGrassi
Sorry, I did not point out htat properly maybe:...

Sorry, I did not point out htat properly maybe: "No output reported, just the processing of the gtf infos."
It finished the processing of the gtf, if you want the number I have to rerun it...but I...
Forum: Bioinformatics 10-10-2012, 05:03 AM
Replies: 6
Views: 1,093
Posted By EGrassi
Thank you for you answer: samtools sort -n...

Thank you for you answer:

samtools sort -n /rogue/bioinfotree/task/RNAseq/dataset/0.1/GSE27003/alignment_tophat/SRR097789.merged.bam SRR097789_sorted
samtools view SRR097789_sorted.bam |...
Forum: Bioinformatics 10-10-2012, 02:23 AM
Replies: 6
Views: 1,093
Posted By EGrassi
htseq-count eats 42G of memory

Hello,

I've been using DESeq for a while and right now htseq-count (version 0.5.3p9) it's giving me problems with a bam file (smaller than other that I've used with the same options and the same...
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