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Forum: Bioinformatics 09-16-2011, 05:40 AM
Replies: 7
Views: 3,593
Posted By Seq84
Yes sure you can use the .bed file. You should...

Yes sure you can use the .bed file. You should have a .bed file with all targeted regions (exons regions). Set in depthofcoverage the option -L exons.bed.
If you want to have a specific coverage (of...
Forum: Bioinformatics 08-03-2011, 01:07 AM
Replies: 7
Views: 8,184
Posted By Seq84
Hi, Reads filled with white have mapping...

Hi,
Reads filled with white have mapping quality score = 0
best regards,
Matteo
Forum: Bioinformatics 07-27-2011, 07:24 AM
Replies: 2
Views: 6,212
Posted By Seq84
Hi all, I have the same problem at point 1. ...

Hi all,

I have the same problem at point 1.

Thanks in advance for any suggestions.
Forum: Bioinformatics 07-02-2011, 11:17 PM
Replies: 42
Views: 104,068
Posted By Seq84
Maybe is the `quote. Try to copy and paste this...

Maybe is the `quote. Try to copy and paste this string:

'@RG\tID:foo\tSM:bar'

Let me know.
Forum: Bioinformatics 05-16-2011, 12:24 AM
Replies: 9
Views: 6,734
Posted By Seq84
Hi all, I'm interested too! Could someone post a...

Hi all, I'm interested too! Could someone post a link or a brief description of BWA quality mapping scoring ?

Thanks in advance.
Forum: Bioinformatics 04-27-2011, 07:22 AM
Replies: 0
Views: 2,843
Posted By Seq84
Fastqc error

Hi all, i'm trying to run fastqc on a fastq file and the application return this error:

Failed to process file: Midline didn't start with "+".

This file is a fastq file obtained from Galaxy...
Forum: Bioinformatics 04-18-2011, 02:24 AM
Replies: 0
Views: 2,575
Posted By Seq84
Post Picard: HsMetrics

Hi all,

I've performed CalculateHsMetrics.jar with Picard and i've noticed that at the coloumn NEAR_BAITS_BASES i've a negative number.
Is it normal?
Moreover, is this report good?
Thanks in...
Forum: Bioinformatics 04-15-2011, 04:53 AM
Replies: 42
Views: 104,068
Posted By Seq84
This is BWA sampe in 0.5.9-r16 version. With -r...

This is BWA sampe in 0.5.9-r16 version.
With -r option followed by such kind of string you could insert RG directly during mapping.

For editing RG lines use AddOrReplaceReadGroup...
Forum: Bioinformatics 04-13-2011, 01:05 AM
Replies: 3
Views: 1,786
Posted By Seq84
Thanks for your reply Heisman, next time will...

Thanks for your reply Heisman, next time will decrease number of cycles!
Forum: Bioinformatics 04-12-2011, 05:37 AM
Replies: 3
Views: 1,786
Posted By Seq84
I'm interesting in this issue too, in our target...

I'm interesting in this issue too, in our target resequencing experiment we detected a wide range of % in duplicates (from 2 to 80 %). Is it normal that in a target reseq experiment % of duplicates...
Forum: Illumina/Solexa 04-08-2011, 04:38 AM
Replies: 5
Views: 3,681
Posted By Seq84
Duplicates percentage in target resequencing

Hi,

We are performing a target resequencing experiment, where we enriched 8 regions.

What's the mean % of duplicates in this kind of experiments ?
The % in duplicates is casual or is...
Forum: Genomic Resequencing 04-08-2011, 04:28 AM
Replies: 1
Views: 2,069
Posted By Seq84
Coverage assessment

Hi,

We are making a target resequencing experiment in 6 differents regions. During coverage assessment with DepthOfCoverage walker in GATK we noticed that regions rich in GC (high %GC) were...
Forum: Bioinformatics 03-24-2011, 06:43 AM
Replies: 14
Views: 7,819
Posted By Seq84
me too i've the same error.. even with...

me too i've the same error.. even with VALIDATION_STRINGENCY=SILENT
Forum: Bioinformatics 03-08-2011, 05:56 AM
Replies: 4
Views: 3,679
Posted By Seq84
Me too i had the same problem of CHRYSES and i've...

Me too i had the same problem of CHRYSES and i've solved with -I option.

Why it happens? is a version problem (0.1.12-10 (r896-r862)) or is a problem internal to the .bam file?

Thanks in...
Forum: Bioinformatics 02-18-2011, 03:05 AM
Replies: 9
Views: 4,726
Posted By Seq84
Yeah this script converts only solexa format and...

Yeah this script converts only solexa format and not illumina(1.3 or 1.5+) one.
Forum: Bioinformatics 02-15-2011, 03:09 AM
Replies: 3
Views: 3,428
Posted By Seq84
I've solved the problem Greetz :)

I've solved the problem

Greetz :)
Forum: Bioinformatics 02-14-2011, 11:56 PM
Replies: 3
Views: 3,428
Posted By Seq84
Maq Segmentation fault

I'm trying to use Maq software but i've face with some problems.

1. Conversion of *qseq.txt files (obtained after demultiplexing) to fastq (illumina) format. For doing this operation i've used...
Forum: Introductions 02-14-2011, 07:11 AM
Replies: 0
Views: 997
Posted By Seq84
Smile Hi from Italy

Hi all,

I'm a newbie in NGS data analysis, actually i'm working on Illumina GA-I data. I hope to learn a lot here.

Greetings :)
Forum: Bioinformatics 02-11-2011, 06:38 AM
Replies: 12
Views: 46,136
Posted By Seq84
Hi all, Me too i've the same problem!! Can...

Hi all,

Me too i've the same problem!! Can anyone suggest a solution?
Thanks in advance
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