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Search: Posts Made By: atma_weapon
Forum: Bioinformatics 12-04-2015, 03:01 PM
Replies: 3
Views: 1,646
Posted By atma_weapon
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...
Forum: Bioinformatics 12-04-2015, 02:48 PM
Replies: 3
Views: 1,646
Posted By atma_weapon
I have the same problem

I have the same problem
Forum: RNA Sequencing 11-13-2014, 05:58 AM
Replies: 3
Views: 1,415
Posted By atma_weapon
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...
Forum: Bioinformatics 11-11-2014, 01:07 AM
Replies: 4
Views: 1,533
Posted By atma_weapon
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...
Forum: Bioinformatics 11-10-2014, 06:27 AM
Replies: 4
Views: 1,533
Posted By atma_weapon
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...
Forum: Bioinformatics 03-13-2014, 04:37 AM
Replies: 4
Views: 6,251
Posted By atma_weapon
ok, it looks like it happened only with 2.2.27,...

ok, it looks like it happened only with 2.2.27, with the new version everything is ok, thanks
Forum: Bioinformatics 03-12-2014, 03:56 PM
Replies: 4
Views: 6,251
Posted By atma_weapon
yes, same result

yes, same result
Forum: Bioinformatics 03-12-2014, 03:35 PM
Replies: 4
Views: 6,251
Posted By atma_weapon
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 ...
Forum: Bioinformatics 09-03-2013, 07:27 AM
Replies: 2
Views: 3,425
Posted By atma_weapon
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...
Forum: Bioinformatics 04-11-2013, 04:22 PM
Replies: 0
Views: 838
Posted By atma_weapon
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...
Forum: RNA Sequencing 02-27-2013, 06:23 AM
Replies: 4
Views: 1,821
Posted By atma_weapon
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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