Forum: Bioinformatics
07-02-2015, 08:36 AM
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Replies: 1
Views: 2,294
Find mates in a SAM file
I want to identify the actual pairs of reads in a SAM file that potentially has multiple alignments for the same given pair.
Is it sufficient to check whether two lines in the SAM file have same...
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Forum: Bioinformatics
02-24-2012, 06:25 PM
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Replies: 10
Views: 6,056
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Forum: Bioinformatics
09-12-2011, 08:23 AM
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Replies: 14
Views: 6,155
I thought that v.0.9 should be able to...
I thought that v.0.9 should be able to distinguish between encodings (see below) ... but I will try to see if the latest version can help.
Thanks!
From the release notes:
"30-3-11: Version...
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Forum: Bioinformatics
09-12-2011, 06:52 AM
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Replies: 14
Views: 6,155
FASTQC guessing wrong quality encoding
Hello,
I have some Illumina files processed with CASAVA 1.8.
The program FASTQC is guessing the format to be be Illumina 1.5
Is there a way to explicitly tell fastqc what encoding the data is?...
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Forum: Bioinformatics
09-09-2011, 07:45 AM
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Replies: 1
Views: 2,005
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Forum: Bioinformatics
09-06-2011, 09:16 AM
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Replies: 4
Views: 4,023
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Forum: Bioinformatics
09-06-2011, 09:02 AM
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Replies: 4
Views: 4,023
dealing with 5' end bias in RNASEQ
Hello,
I read about random hexamer priming bias in Illumina RNASEQ (see Hansen et al., NAR 2010, vol 38 no 12). Specifically, "There is a strong distinctive pattern in the nucleotide frequencies...
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Forum: Bioinformatics
08-10-2011, 07:35 AM
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Replies: 5
Views: 8,363
comparing results by cuffdiff, edgeR, DESeq
Has anyone tried to compare the results from the various tools that offers differential expression analyses for RNASEQ data?
I understand they have different underlying models and assumptions, but...
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Forum: Bioinformatics
08-02-2011, 12:01 PM
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Replies: 9
Views: 2,469
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Forum: Bioinformatics
08-02-2011, 11:29 AM
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Replies: 9
Views: 2,469
I used edgeR to determine the list of...
I used edgeR to determine the list of up-regulated and down-regulated genes. I have 3 samples, so in total I have 6 lists. The number of genes for each list is:
388 edger_1_down.genelist
503...
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Forum: Bioinformatics
08-02-2011, 09:59 AM
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Replies: 9
Views: 2,469
GO enrichment RNASEQ: nothing!
Hello,
I used goseq package to do GO-enrichment of RNASEQ data. The up- and down-regulated genes are not enriched in any category if I use the BH (FDR) correction. Is that a possible situation or...
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Forum: Bioinformatics
07-19-2011, 10:18 AM
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Replies: 3
Views: 3,981
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Forum: Bioinformatics
07-05-2011, 02:15 PM
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Replies: 5
Views: 4,590
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Forum: Bioinformatics
07-05-2011, 11:25 AM
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Replies: 3
Views: 7,752
fastqc - overrepresented sequences
I have run a FASTQC analysis and found out that there are hundreds of over-represented sequences in my datasets. Some of these, are Illumina PCR primers, some are single end adapters.
Does it...
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Forum: Bioinformatics
06-21-2011, 10:14 AM
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Replies: 0
Views: 2,804
clustering RNASeq data
Hi,
I would like to do some lustering of rnaseq data.
I used tophat/cuffdiff to get a table with the fpmk values.
Beside the quantile normalization option in cuffdiff, what other trick has to be...
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Forum: Bioinformatics
06-17-2011, 12:11 PM
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Replies: 0
Views: 2,194
library complexity for RNASEQ
How can I establish whether my library has a good complexity? What percentage of the reads should be unique?
Thanks!
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Forum: Bioinformatics
06-14-2011, 12:07 PM
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Replies: 1
Views: 4,254
cuffdiff with biological replicates
The FPKM values reported by CUFFDIFF when the samples have biological replicates correspond to the average value across the replicates?
Thanks in advance
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Forum: Bioinformatics
05-27-2011, 10:04 AM
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Replies: 3
Views: 2,407
cuffdiff count tables
I tried the option to emit count tables in cuffdiff. I expected the counts to be integers, but I get fractions. Are these normalized counts?
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Forum: Bioinformatics
05-23-2011, 01:57 PM
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Replies: 4
Views: 2,266
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Forum: Bioinformatics
05-20-2011, 02:12 PM
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Replies: 4
Views: 2,266
Thank you, HESmith!
The barcodes are in the...
Thank you, HESmith!
The barcodes are in the header so I am assuming I cannot use the utility in fastx_toolkit.
Does it make sense to list all possible barcodes that would be acceptable (i.e....
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Forum: Bioinformatics
05-20-2011, 12:15 PM
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Replies: 4
Views: 2,266
non-matching barcodes
Hi,
I have some RNASEQ data from Illumina 1.4+ pipeline.
The barcodes of a multiplex run are appended to the header line of the fastq file. I supposedly have two samples in there, so I am...
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Forum: Bioinformatics
04-21-2011, 12:38 PM
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Replies: 2
Views: 3,782
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Forum: Bioinformatics
04-13-2011, 07:38 AM
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Replies: 4
Views: 2,601
Hi,
You are right. It would make more sense...
Hi,
You are right. It would make more sense to separate TopHat from Cufflinks. I guess my intention was to pinpoint to some kind of alignment tools with or without transcriptome assembly tool.
...
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Forum: Bioinformatics
04-13-2011, 06:18 AM
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Replies: 0
Views: 1,223
Does the TopHat illumina quality option work?
I was never able to get the "--solexa1.3-quals" option to work. When I manually convert quality and then run TopHat everything is ok, but when I skip the manual conversion, I always get an error...
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Forum: Bioinformatics
04-13-2011, 06:14 AM
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Replies: 4
Views: 2,601
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