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Forum: RNA Sequencing 03-14-2014, 12:53 PM
Replies: 0
Views: 2,416
Posted By angerusso
Thumbs down tophat: definition of spanning mate pair

I have found a reference where the "encompassing" read and "spanning" reads are being clearly distinguished and well defined.
...
Forum: RNA Sequencing 02-07-2014, 11:46 AM
Replies: 0
Views: 1,512
Posted By angerusso
Wrong exon number information from tophat-fusion

I posted this question in "BioInformatics" as well to someone who experienced similar problem with no answers. Any solutions from the RNASequencing forum?

It appears to me that somehow tophat...
Forum: Bioinformatics 02-07-2014, 11:42 AM
Replies: 1
Views: 1,543
Posted By angerusso
messed up exon information from tophat-fusion

I also experienced similar problem with well known fusion.

Expected fusion in my sample is TMPRSS2(Exon1) with ERG. What I obtain is TMPRSS2 (exon14) with ERG which doesn't make sense.

Is there...
Forum: Bioinformatics 11-11-2013, 06:10 PM
Replies: 2
Views: 3,306
Posted By angerusso
Smile difference between rr ff and rf reads

Hi:

I am wondering which fusion should I prioritize from a couple of candidates.

As you know tophat fusion generates a list with the direction of fusion mentioned as well. I am not a biologist...
Forum: RNA Sequencing 08-26-2013, 11:32 AM
Replies: 1
Views: 1,617
Posted By angerusso
Question how to look for known fusion in fastq file

Hello:

I have an internal data for NCI-h660 file with 8m mapped pairs (HiSeq, 50bp paired end data) and I have an external dataset (4m mapped pairs, 50 bp paired end generated on GAII).
...
Forum: RNA Sequencing 08-15-2013, 12:24 PM
Replies: 9
Views: 4,464
Posted By angerusso
Ignore my previous msg. My files are same size...

Ignore my previous msg. My files are same size when I used "du -b" command.
Forum: RNA Sequencing 08-15-2013, 12:02 PM
Replies: 9
Views: 4,464
Posted By angerusso
So I ran the following perl script: ...

So I ran the following perl script:

https://bitbucket.org/jesseerdmann/fairview-galaxy-dist/raw/8e6e7a346284c7c261c951998b0138e82f540f43/tools/msi/pe-sync-2-files.pl

and it says: "passed full...
Forum: RNA Sequencing 08-15-2013, 09:14 AM
Replies: 9
Views: 4,464
Posted By angerusso
Yes my data is paried end. Another complication...

Yes my data is paried end. Another complication is that the two pairs are of unequal size.

du -s command gives:
*_R1* = 64850642
*_R2* = 48640554
Forum: RNA Sequencing 08-15-2013, 08:49 AM
Replies: 9
Views: 4,464
Posted By angerusso
how to randomly select 20m reads out of a FASTQ file

Hi All,

I have an RNASeq data from which I need to randomly select 20 million reads, around 5 times. The whole file is about 200m reads.

What is a way to do this? Does anyone have a script to...
Forum: RNA Sequencing 07-28-2013, 04:52 PM
Replies: 1
Views: 1,414
Posted By angerusso
Question: prioritizing fusion based on tophat result

How to prioritize fusions based on these columns?

Potential_fusions written by tophat-fusion-post writes these 5 columns but I don't what these columns really mean. Can anyone explain? E.g. I...
Forum: RNA Sequencing 07-03-2013, 10:11 AM
Replies: 0
Views: 1,346
Posted By angerusso
identifying common reads between mouse and human alignments

Hi,

I have some rnaseq data from xenograft models. I am aligning the reads to human genome and mouse genome separately.

the idea is to throw the reads that are mapped to both human and mouse....
Forum: RNA Sequencing 06-11-2013, 11:34 AM
Replies: 1
Views: 2,572
Posted By angerusso
Angry genes.fpkm_tracking (Coverage column)

In the genes.fpkm_tracking file, why is the "coverage" for the gene not reported from cufflinks?

I understand to get the fpkm_per_gene, transcript level fpkm is summed up. How about coverage...
Forum: RNA Sequencing 06-09-2013, 06:02 PM
Replies: 2
Views: 1,936
Posted By angerusso
Angry memory error: tophat-fusion-post

I have ~400 samples where I ran tophat2 fusion. Now I am trying to run tophat-fusion-post which gives the following error:

Traceback (most recent call last):
File...
Forum: RNA Sequencing 05-05-2013, 08:10 PM
Replies: 3
Views: 4,525
Posted By angerusso
Error with RNA-SeQC

Hi,

I used following 4 steps to get sequencing statistics from RNASeqC but I get error, could anyone help me understand and get rid of this error?

Thanks.

RNA-SeQC v1.1.7 05/14/12
Creating...
Forum: RNA Sequencing 04-29-2013, 12:44 PM
Replies: 0
Views: 1,383
Posted By angerusso
Unhappy tophat2 and cufflinks with and without --fusion-search

Hello,

I have a question about using tophat2 with and without --fusion-search options for 5 cell lines of interest:

1. Is "accepted_hits.bam" file output the same with and without...
Forum: Bioinformatics 04-23-2013, 08:09 AM
Replies: 34
Views: 13,991
Posted By angerusso
Thanks very much, I am able to get it to work...

Thanks very much, I am able to get it to work after modification.
Forum: Bioinformatics 04-22-2013, 09:51 AM
Replies: 34
Views: 13,991
Posted By angerusso
how to modify 1.fq to write bamfilename_1.fq?

Hi Richard,

How can I modify "1.fq" and "2.fq" to write instead bamfilename_1.fq and bamfilename_2.fq as I have many bam files and I want to preserve the name of the file where fastq files are...
Forum: RNA Sequencing 04-16-2013, 01:13 PM
Replies: 0
Views: 1,604
Posted By angerusso
Question Estimate tophat2 parameters from rnaseq data?

I have some pre-computed bam files which I need to run tophat2 fusion search. Can anyone guide me as to how to use these RNA metrics to determine tophat2 parameters e.g. mate_inner_dist,...
Forum: RNA Sequencing 04-15-2013, 01:02 PM
Replies: 5
Views: 2,108
Posted By angerusso
Question Hi Daniel, I am referring to the 27 fusions...

Hi Daniel,

I am referring to the 27 fusions that are mentioned to be known and/or validated by RT-PCR as mentioned in the paper.

I didn't use the same version of software as in the paper. I...
Forum: RNA Sequencing 04-15-2013, 09:03 AM
Replies: 5
Views: 2,108
Posted By angerusso
Missing 4 fusions using tophat2

Hi Daniel,

It seems you mis understood my question. the question was how to modify tophat2 or tophat-fusion-post parameters to find the 4 missing fusions which were found using previous versions...
Forum: RNA Sequencing 04-14-2013, 08:59 PM
Replies: 5
Views: 2,108
Posted By angerusso
Exclamation tophat2: missed 5/27 breast cancer cell line fusions

I missed 2 BT474 and SKBR3 fusions using tophat2. I think I was supposed to find 25/27 of these fusions according to tophat paper. Can anyone help me with why could this be? See below my parameters:...
Forum: RNA Sequencing 04-02-2013, 07:32 AM
Replies: 5
Views: 2,772
Posted By angerusso
tophat-fusion-post: KeyError: 'score'

Hello, I am tophat-fusion-post. My job ran fine until the very end where I get the error ("Score") as below.

I get 6898 fusions in potential_fusion.txt with the command:

> tophat-fusion-post -p...
Forum: Bioinformatics 03-05-2012, 07:43 AM
Replies: 0
Views: 2,262
Posted By angerusso
Question "Bcftools mpileup" removes marked duplicates?

Hey,

My question is does samtools mpileup automatically removed duplicates from test.marked.bam output from Picard/MarkDuplicates?

I used Picard Tools to create: test.marked.bam

Then I use ...
Forum: Bioinformatics 02-28-2012, 05:59 PM
Replies: 2
Views: 2,266
Posted By angerusso
Unhappy How to set filter for frequency of reads AND HapMap exome sample results:

Hey All,

I only used so far three filters for my whole exome pipeline (aligning to hg19) for a HapMap sample. I tried it on the NA19240 Hapmap sample from paper below (Table 3) which shows ~196...
Forum: Bioinformatics 02-19-2012, 06:04 PM
Replies: 0
Views: 1,329
Posted By angerusso
Exclamation Marking duplicates and comparing 2 WE samples?

Hey,

Two follow-up questions for my WholeExome Analysis: :p

1) I used Picard "MarkDuplicates" to mark duplicates and called bam as "marked.bam". I used snpeff to annotate snps and indels etc....
Showing results 1 to 25 of 47

 


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