Forum: Bioinformatics
12-04-2015, 03:01 PM
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Replies: 3
Views: 1,646
I ran gsnap with default parameters for...
I ran gsnap with default parameters for mismatched (my reads are 75bp) and it should be((readlength+2)/kmer - 2) mismatches
But sometimes I get up to 15 mismatches per reads. They are usually lumped...
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Forum: Bioinformatics
12-04-2015, 02:48 PM
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Replies: 3
Views: 1,646
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Forum: RNA Sequencing
11-13-2014, 05:58 AM
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Replies: 3
Views: 1,415
alternative splicing detection from one sample
hello, I would like to know if it is possible to check if in a rna-seq there are alternative splicing events, not comparing two condition but inside one condition only, that is if different...
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Forum: Bioinformatics
11-11-2014, 01:07 AM
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Replies: 4
Views: 1,533
thank you, I have noticed that the company...
thank you, I have noticed that the company assembled the 3 sample into a consensus reference transcriptome, and later they provided a SNP call for each sample comparing it against this reference, is...
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Forum: Bioinformatics
11-10-2014, 06:27 AM
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Replies: 4
Views: 1,533
SNP calling and no reference genome
Hello, We have sequenced (RNA sequencing) three different strain of the same tree species (living in three different geographic locations) with the intention of discovering SNPs between the three...
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Forum: Bioinformatics
03-13-2014, 04:37 AM
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Replies: 4
Views: 6,251
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Forum: Bioinformatics
03-12-2014, 03:56 PM
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Replies: 4
Views: 6,251
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Forum: Bioinformatics
03-12-2014, 03:35 PM
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Replies: 4
Views: 6,251
blast evalue strange behaviour
hello, I am experiencing a strange behaviour of blastn with the option "evalue":
$ blastn -task blastn -query _p -db genome.fa -outfmt 6 ...
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Forum: Bioinformatics
09-03-2013, 07:27 AM
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Replies: 2
Views: 3,425
Go terms enrichment visualization
hello, I have a list of Go terms enrichments of a RNAseq differential expression, in the way "GOterm: p-value", I would like to know if there exists a tool for a cool visualization of these results...
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Forum: Bioinformatics
04-11-2013, 04:22 PM
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Replies: 0
Views: 838
calculate alignement differences
hello, I would like to know if there is a way to determine whether two set of data from rna seq are significantly different, like these:
2146
for example, the first two rows are similar, while...
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Forum: RNA Sequencing
02-27-2013, 06:23 AM
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Replies: 4
Views: 1,821
gsnap produces more reads than fastq
hello, i am running gsnap with rna seq data against a reference genome:
gsnap -m 10 -B 5 -t 8 -A sam -d GENOME seqs.fastq > res.sam
but strangely, the output sam file contains more reads than...
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