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Forum: Bioinformatics 08-19-2012, 05:11 PM
Replies: 0
Views: 1,120
Posted By EBER
Cufflinks: transcript reconstruction of known isoforms using a reference database

I have a few questions regarding splice isoform reconstruction, when using a reference database, 400,000 millions paired-end reads and 2 biological replicates. In other words, a very good coverage....
Forum: Bioinformatics 07-25-2012, 06:13 AM
Replies: 4
Views: 1,139
Posted By EBER
paired-end and Scripture

Hello, I am slowly getting my hands on Scripture and have stumbled on yet another unclear (at least to me )detail. I have paired-end data and the two pairs are in a sigle TopHat-derived *.bam file. I...
Forum: RNA Sequencing 07-11-2012, 06:17 PM
Replies: 1
Views: 1,220
Posted By EBER
Scripture genome/chromosome.fa file

Question about Scripture.
Does Scripture only reconstruct transcripts one Chromosome at a time?
EBER
Forum: Bioinformatics 06-08-2012, 07:56 AM
Replies: 1
Views: 2,738
Posted By EBER
samtools sort

Hello,
I am trying to sort a large bam file, actually split in two, with samtools sort
I use -m 10000000000 so the job creates 8 sorted files of about the same size, plus a smaller last one.
At...
Forum: Bioinformatics 05-26-2012, 03:59 PM
Replies: 0
Views: 823
Posted By EBER
how to display cuffdiff tracking files

Hello:
I am new to this and have made it all the way to producing Cuffdiff outputs.
At this point I am stuck, because I cann't find out how to display Cuffdiff tracking files (FPKM values) as...
Forum: Bioinformatics 05-25-2012, 04:06 PM
Replies: 0
Views: 1,250
Posted By EBER
relating Cuffdiff test id to actually transcript id

Hello,

I have a "beginner's" question, which I failed to answer myself.
In the Cuffdiff outputs, how do I find out which transcript isoform corresponds to each Test id?

Thanks,
EBER
Forum: Bioinformatics 05-25-2012, 05:09 AM
Replies: 2
Views: 1,185
Posted By EBER
Thanks for you answer!

Thanks for you answer!
Forum: Bioinformatics 05-24-2012, 05:23 PM
Replies: 2
Views: 1,185
Posted By EBER
TopHat doesnt handle 450million reads

Hello I am analyzing a couple of paired-end datasets (75bp), each containing about 450 million reads.
TopHat 1.4.1 does well, as long as I have the "--non-novel-juncs" flag.
TopHat 2 however, FAILs...
Forum: Literature Watch 05-03-2012, 05:24 AM
Replies: 1
Views: 2,039
Posted By EBER
mean inner distance

I am new to RNA-seq data analysis and have a question about how to calculate the mean inner distance to input in TopHat.
I am dealing with 75bp paired-end reads, 300 fragments and 120bp total...
Forum: Bioinformatics 05-02-2012, 07:17 PM
Replies: 0
Views: 1,606
Posted By EBER
Illumina 1.8 and TopHat

Hello
I was recently told that that FASTQ data from Illumina 1.8 or higher no longer has to be converted to Sanger FASTQ. Furthermore, that FASTQ Quality Filter is not necessary either because...
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