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Search: Posts Made By: Gianza
Forum: Bioinformatics 04-22-2013, 01:42 PM
Replies: 7
Views: 5,716
Posted By Gianza
Reading the Bowtie2 manual, it seems that the...

Reading the Bowtie2 manual, it seems that the AS:i: flag reports the score for the best alignment, while XS:i the score for the second-best one. Thus one could compare these two value to figure out...
Forum: Bioinformatics 08-24-2010, 08:12 AM
Replies: 11
Views: 4,409
Posted By Gianza
I don't know you might be interested, but Mosaik...

I don't know you might be interested, but Mosaik allows every threshold you want; then the only discrimination become that reads must align to only one place. (-m unique)

Hope might help
Forum: Bioinformatics 08-24-2010, 08:06 AM
Replies: 0
Views: 1,582
Posted By Gianza
Unhappy Mosaik, gigaBayes and paired-end output

Hello everybody,
I'm facing a weird problem, really hope that somebody can help me.

I have aligned both 454 and Solexa paired-ends reads on a transcriptome reference for SNP mining purposes.
...
Forum: Bioinformatics 07-23-2010, 10:08 AM
Replies: 16
Views: 10,795
Posted By Gianza
Novoalign seems to have an internal-only trimming...

Novoalign seems to have an internal-only trimming pipeline.
Looking at the manual it doesn't seem it will just return a trimmed fastq, but the final alignment....Am I wrong?

I would like to avoid...
Forum: Bioinformatics 07-23-2010, 10:05 AM
Replies: 16
Views: 10,795
Posted By Gianza
I'm using this command. I want to clarify I'm...

I'm using this command.
I want to clarify I'm not a bioinformatician.

fastx_clipper -a AAGCAGTGGTATCAACGCAGAGTACGCGGG -i 1M_1.txt -M 20 -n -o output.txt

For Adrian_H: could you please give me...
Forum: Bioinformatics 07-23-2010, 07:56 AM
Replies: 16
Views: 10,795
Posted By Gianza
Fastq adaptors removal/stripping/cleaning

Hi guys,
I'm facing such a very dumb problem.
I cannot find a tool which simply strip off adaptors from Fastq Illumina files. I have contamination from library synthesis adaptors (SMART)....
Forum: Bioinformatics 04-30-2010, 02:13 AM
Replies: 4
Views: 2,642
Posted By Gianza
Hello everybody, I'm struggling with the same...

Hello everybody,
I'm struggling with the same problem.
I'm on the way to buy a desktop/workstation.
My project is the following- eukaryote-plant
-454 EST assembly 1,5 M reads from 3 different...
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