Forum: Bioinformatics
08-21-2020, 06:59 AM
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Replies: 2
Views: 874
Paired end seq read lengths are different
Hi all,
I recently acquired a dataset from GEO (HiSeq 2500, accession: GSE107029). It is a paired-end but the read_1 is 94 bp while read_2 is 100 bp. Since I've never seen paired-end data with...
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Forum: Bioinformatics
05-28-2014, 05:45 PM
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Replies: 1
Views: 1,185
I figured out -a 6 parameter issue. It does not...
I figured out -a 6 parameter issue. It does not ensure individual read to have at least x bps on each side of junction. Instead, it ensures that each junction to have at least one read that meet the...
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Forum: Bioinformatics
05-28-2014, 04:43 PM
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Replies: 1
Views: 1,185
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Forum: RNA Sequencing
04-29-2014, 05:06 PM
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Replies: 1
Views: 1,702
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Forum: Bioinformatics
08-26-2013, 10:40 AM
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Replies: 2
Views: 1,755
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Forum: Bioinformatics
08-23-2013, 03:03 PM
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Replies: 2
Views: 1,755
gene fusion question
Dear all,
I am new to the gene fusion field and I would like to ask a basic question.
What is a good and easy program to use to detect gene fusion form RNA-Seq data?
Thank you in advance,...
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Forum: RNA Sequencing
09-10-2012, 12:35 PM
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Replies: 2
Views: 3,184
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Forum: Bioinformatics
02-01-2012, 01:23 PM
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Replies: 5
Views: 4,330
I agree that we'd better stick to cuffdiff for...
I agree that we'd better stick to cuffdiff for differentially expressed gene analysis. Doe cuffdiff have "paired"-analysis feature for the data with replicates? The paired-analysis feature is the...
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Forum: Bioinformatics
02-01-2012, 12:09 PM
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Replies: 5
Views: 4,330
Cufflinks, differentially expressed genes
Hi,
I am trying to run edgeR or DEGseq using the output from cufflinks.
I usually use mapped reads count as an input to edgeR or DEGseq. What cufflinks output do I need to use for an input to...
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Forum: Bioinformatics
11-19-2009, 08:12 AM
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Replies: 1
Views: 2,512
Running TopHat with 32bp or 36bp reads
Hi all,
I am trying to run TopHat with 32bp or 36bp reads. I am setting the length of segments to the half of the original length (16bp for 32bp reads and 18bp for 36bp reads). Besides it takes...
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Forum: Bioinformatics
11-04-2009, 12:08 PM
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Replies: 1
Views: 2,267
TopHat questions
Hi,
I have a few general questions.
I am planning to do the junction mapping using 76bp reads.
What is the good anchor length to use (I am currently using 5 with a -5 option)?
Since the...
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Forum: Bioinformatics
10-02-2009, 08:39 AM
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Replies: 1
Views: 3,287
Bowtie output
Hi all,
I got an RNA seq file that contains about 15million reads.
As it has more than 32bp reads, I decided to use Bowtie instead of my usual pick which is Eland.
So I mapped the sequence on...
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Forum: Bioinformatics
09-17-2009, 01:53 PM
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Replies: 3
Views: 7,939
wiggle or bedGraph
Hi all,
I have about 300,000 lines of data I want to add to UCSC genome browser as a custom track.
Few lines of the data I have are:
=======
Chr Start End ...
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Forum: RNA Sequencing
09-17-2009, 09:27 AM
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Replies: 2
Views: 3,040
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Forum: Bioinformatics
09-15-2009, 09:36 AM
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Replies: 7
Views: 6,039
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Forum: Bioinformatics
09-15-2009, 08:20 AM
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Replies: 7
Views: 6,039
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Forum: Bioinformatics
09-15-2009, 07:10 AM
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Replies: 7
Views: 6,039
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Forum: RNA Sequencing
09-14-2009, 02:38 PM
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Replies: 2
Views: 2,734
Using tophat results via UCSC genome browser
Hi all,
Recently, I ran TopHat with 76bp reads data and got the results (sam, bed, and wig files).
Actual a few lines of my input (fasta file) are:
>HWUSI-EAS366:4:1:4:624#0/1:...
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Forum: Bioinformatics
09-09-2009, 12:06 PM
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Replies: 1
Views: 2,723
TopHat questions (indexes and seq length)
Hi all,
I just downloaded and installed tophat with bowtie.
Using the test_data, it worked fine and found some junctions.
I went ahead and ran Chris Burge's cerebellum data (12M reads, 36bp)...
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