SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 22 of 22
Search took 0.00 seconds.
Search: Posts Made By: Lizex
Forum: RNA Sequencing 10-04-2013, 08:40 AM
Replies: 9
Views: 5,398
Posted By Lizex
Yes I guess that could be the problem. In my case...

Yes I guess that could be the problem. In my case the annotation file is not good enough. I'm working on something. Send me an e-mail.
Forum: RNA Sequencing 10-04-2013, 01:12 AM
Replies: 9
Views: 5,398
Posted By Lizex
Hi 11xinqi I also got no name for the gene but...

Hi 11xinqi
I also got no name for the gene but this is what I do to get my transcripts annotated:
Take the gene_exp.diff file open with TextEdit, save as text; use command: grep yes gene_exp.txt >...
Forum: RNA Sequencing 10-02-2013, 09:25 AM
Replies: 9
Views: 5,398
Posted By Lizex
Hi 11xingi Its not a problem. It happened...

Hi 11xingi
Its not a problem. It happened because one of the conditions had zero and dividing by zero gives you "inf" for infinity.
Forum: RNA Sequencing 09-15-2013, 11:59 AM
Replies: 9
Views: 5,398
Posted By Lizex
Genes and transcripts have expression levels of zero or "nan or "inf"

Hi All
I don't know whether somebody else has experience a similar problem.
I'm experiencing the following problem using the pre-compiled binary packages of Tophat-2.0.9 and Cufflinks-2.1.1 where...
Forum: Bioinformatics 09-04-2013, 07:24 AM
Replies: 25
Views: 12,539
Posted By Lizex
Thanks GenoMax for your suggestions. I finally...

Thanks GenoMax for your suggestions. I finally got the pre-compiled binary to work.
Forum: Bioinformatics 09-04-2013, 12:06 AM
Replies: 25
Views: 12,539
Posted By Lizex
Hi Genomax I'm using a Mac OS 10.6.8 Xcode...

Hi Genomax

I'm using a Mac OS 10.6.8 Xcode 3.2.3

Command to compile tophat-2.0.9
./configure --prefix=/Users/lhusselmann/bin/tophat-2.0.9 --with-boost=/usr/local/Cellar/boost...
Forum: Bioinformatics 09-03-2013, 01:59 PM
Replies: 25
Views: 12,539
Posted By Lizex
Hi Ahmetz I have compiled and installed...

Hi Ahmetz
I have compiled and installed Tophat-2.0.9 and got this error on the test_data provided on Tophat website. The same test data run with tophat work, but with tophat2 it gives the error...
Forum: RNA Sequencing 08-29-2013, 06:37 AM
Replies: 49
Views: 31,523
Posted By Lizex
Thanks for the advice.

Thanks for the advice.
Forum: RNA Sequencing 08-29-2013, 03:23 AM
Replies: 49
Views: 31,523
Posted By Lizex
Thanks for the reply. This result was for the...

Thanks for the reply. This result was for the paired reads (output from Trimmomatic). What should I do for the unpaired reads (output from Trimmomatic) which don't have an even number of reads, read1...
Forum: RNA Sequencing 08-29-2013, 02:43 AM
Replies: 49
Views: 31,523
Posted By Lizex
Hi dpryan I've tried Trimmomatic. The number...

Hi dpryan

I've tried Trimmomatic. The number of reads i.e read1.fq and read2.fq are 1 492 345 for each. After mapping using Tophat 1.4.0, the stats of the accepted_hits.bam file looks like this:
...
Forum: RNA Sequencing 08-27-2013, 02:15 PM
Replies: 49
Views: 31,523
Posted By Lizex
Thanks. I'll give it a try.

Thanks. I'll give it a try.
Forum: RNA Sequencing 08-27-2013, 01:24 PM
Replies: 49
Views: 31,523
Posted By Lizex
Thanks, dpryan. What do suggest I use?

Thanks, dpryan. What do suggest I use?
Forum: RNA Sequencing 08-27-2013, 01:22 PM
Replies: 49
Views: 31,523
Posted By Lizex
Why low mapping

Thanks for the reply. I removed adaptors from the reads with cutadapt. I'm also curious how the reads map. Attached please see pic for how these map and also the presence of such a lot of N's. Should...
Forum: RNA Sequencing 08-27-2013, 06:14 AM
Replies: 49
Views: 31,523
Posted By Lizex
RNA-Seq reads mapping very low

Hi All
I have been mapping reads generated on a MiSeq instrument (150bp) against the apple genome. Reads were processed (trimmed and filtered using the fastx_toolkit). Reads mapped are over a 100bp...
Forum: Bioinformatics 08-21-2013, 09:23 AM
Replies: 11
Views: 7,712
Posted By Lizex
Tophat gzip program not found

Thanks guys.

I downloaded the gzip and put it in my PATH. It seems to have done the trick.

Cheers

Lizex
Forum: Bioinformatics 08-21-2013, 07:28 AM
Replies: 11
Views: 7,712
Posted By Lizex
Tophat gzip program not found

Hi SDiehl
Did you get a solution for your problem you had regarding Tophat not opening gzip. I think I have a similar problem. I have compiled and installed Tophat2. When running tophat on the...
Forum: RNA Sequencing 03-26-2013, 12:15 AM
Replies: 38
Views: 17,595
Posted By Lizex
Hi Kenietz Thanks for the reply. I've send...

Hi Kenietz
Thanks for the reply.
I've send the my e-mail adress.

Regards
Forum: RNA Sequencing 03-20-2013, 02:07 AM
Replies: 38
Views: 17,595
Posted By Lizex
Hi Kenietz I've tried to implement what...

Hi Kenietz

I've tried to implement what you've suggested by adding the extra lines to samtools-0.1.18, saving it as samtools_ndsm and re-compiling it by cd into the bin where I keep samtools,...
Forum: RNA Sequencing 02-17-2013, 11:48 PM
Replies: 0
Views: 1,755
Posted By Lizex
Need help in mapping Single end and paired-end reads

Dear all

I have in my project single end reads (100 bp) for some samples and paired end reads (100 bp frw and rev) for the other samples. I had to re-sequence some of the samples of which I have...
Forum: RNA Sequencing 11-16-2012, 12:17 AM
Replies: 67
Views: 72,449
Posted By Lizex
Thanks sdriscoll for the reply. I think I've...

Thanks sdriscoll for the reply.
I think I've discovered my error. Initially I ran this command:
cufflinks -p 8 -N -v -o C2_Cufflinks_output accepted_hits.bam,
without the -N option and gave me 0...
Forum: RNA Sequencing 11-14-2012, 12:47 AM
Replies: 67
Views: 72,449
Posted By Lizex
Hi all Im a newby to RNA-Seq. I've been running...

Hi all
Im a newby to RNA-Seq. I've been running tophat on my data sets and used the accepted_hits.bam file in cufflinks. I used the default parameters. In the output file of cufflinks i.e...
Forum: Bioinformatics 01-26-2012, 11:21 PM
Replies: 0
Views: 2,393
Posted By Lizex
Bioperl Script to convert fasta to fq

Hi pkerrwall your answer to this question:

The problem with this script is that it returns the reference DNA sequence (from the genome fasta file used for mapping) for the transcripts and not the...
Showing results 1 to 22 of 22

 


All times are GMT -8. The time now is 06:42 AM.


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