Forum: Bioinformatics
07-26-2014, 10:42 PM
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Replies: 3
Views: 2,636
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Forum: Bioinformatics
07-22-2014, 10:00 PM
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Replies: 3
Views: 2,636
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Forum: RNA Sequencing
12-30-2013, 02:08 AM
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Replies: 17
Views: 15,506
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Forum: RNA Sequencing
12-30-2013, 12:24 AM
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Replies: 17
Views: 15,506
Hello all,
Anyone has an idea how to count...
Hello all,
Anyone has an idea how to count in tophat2 bam file the uniquely mapped reads?
Tophat(1) had mapping quality of 255 for uniquely mapping. Tophat2 has changed that, and I don't manage...
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Forum: Bioinformatics
08-31-2013, 11:01 PM
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Replies: 9
Views: 4,824
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Forum: Bioinformatics
08-25-2013, 10:12 PM
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Replies: 4
Views: 3,087
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Forum: Bioinformatics
08-25-2013, 10:58 AM
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Replies: 4
Views: 3,087
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Forum: Bioinformatics
07-09-2013, 03:11 AM
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Replies: 2
Views: 1,175
Thanks a lot for the reply.
Yes I meant using...
Thanks a lot for the reply.
Yes I meant using the SizeFactors only for normalization due to different coverage between the samples.
I know one must have replicate - but still don't have them all :)
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Forum: Bioinformatics
07-08-2013, 10:54 PM
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Replies: 2
Views: 1,175
DESeq without replicates
Hello all,
Does DESeq use replicate info in estimateSizeFactors?
For RNA seq without replicates - will it be OK to normalize the data using:
estimateSizeFactors
(and then dividing each column...
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Forum: Bioinformatics
11-15-2012, 11:00 PM
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Replies: 0
Views: 1,017
small RNA seq coverage
Hi all,
Anyone has recommendation for the coverage that is needed when sequencing small RNA seq, for micro RNAs in human/mouse, using Illumina?
Thanks.
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Forum: Bioinformatics
07-16-2012, 06:24 AM
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Replies: 0
Views: 1,319
cutadapt problem
Hi all,
I have the following problem with cutadapt: I ask to remove an adapter only once, but it removes it more than once.
The read:
TTCCACTTGAGTCCAGGGTGCGTACGCTGCAGGTCGACTCCAC
The...
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Forum: Bioinformatics
06-12-2012, 06:37 AM
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Replies: 0
Views: 1,450
whole genome sequencing of mouse genome
Hi all,
Does anybody know what is the number of reads (and what coverage per base) which are needed for sequencing of mouse whole genome - in order to detect translocations, using Illumina...
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Forum: Bioinformatics
02-22-2012, 11:19 PM
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Replies: 12
Views: 3,758
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Forum: Bioinformatics
02-18-2012, 10:50 PM
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Replies: 3
Views: 2,669
TopHat and cufflinks of non-strand-specific reads
Hi all,
I have questions regarding the strand info after TopHat and Cufflinks in NON-strand-specific experiments. I tried to look for the answers in the forum and in the web – but did not manage,...
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Forum: Bioinformatics
10-02-2011, 04:09 AM
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Replies: 9
Views: 4,738
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Forum: Bioinformatics
09-28-2011, 02:50 AM
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Replies: 9
Views: 4,738
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Forum: Bioinformatics
09-23-2011, 10:46 AM
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Replies: 9
Views: 4,738
Thanks for the replies.
Very good questions.
...
Thanks for the replies.
Very good questions.
1. I haven't tried giving the same set twice. Anyway - I wouldn't like to have such differences - no matter where they come from.
2. Regarding the...
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Forum: Bioinformatics
09-23-2011, 07:14 AM
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Replies: 9
Views: 4,738
After running the 2 sets I used cuffcompare to...
After running the 2 sets I used cuffcompare to combine all together. So cuffdiff was run with the same gtf for setA and setB.
I also ran cuffdiff for setA and setB on refseq gtf, and did not get...
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Forum: Bioinformatics
09-22-2011, 02:26 AM
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Replies: 9
Views: 4,738
Cufflinks: a problem with the FPKM ratios?
Hi all,
I am getting inaccurate FPKM ratios after cufflinks. The same samples give low correlations of log 2 ratios (see attached scatter plot), which is very worrying.
Is this a bug in cufflinks...
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Forum: Bioinformatics
09-06-2011, 12:24 AM
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Replies: 3
Views: 2,602
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Forum: Bioinformatics
09-05-2011, 12:00 PM
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Replies: 3
Views: 2,602
detecting alternative splicing in RNA-seq
Hello,
In RNA seq analysis - I have aligned reads to the genome and estimated the abundance of known transcripts in each sample.
In the next step I would like to find genes which their "exon...
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Forum: General
08-31-2011, 11:44 PM
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Replies: 2
Views: 1,686
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Forum: Bioinformatics
08-22-2011, 05:18 AM
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Replies: 0
Views: 1,649
Scripture workflow
Hello,
I would like to use scripture in RNA seq experiments.
I thought of the following work-flow:
1. Align reads with Tophat.
2. For each biological sample separately: run scripture with...
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Forum: Bioinformatics
06-14-2011, 05:01 AM
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Replies: 6
Views: 4,134
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Forum: Bioinformatics
06-14-2011, 03:36 AM
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Replies: 6
Views: 4,134
Thanks a lot!
My data is in fpkm (after...
Thanks a lot!
My data is in fpkm (after cufflinks and cuffdiff). Is this an appropriate input to DESeq?
With such values - can I use DESeq to check for differential expression and to cluster the...
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