SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 26
Search took 0.00 seconds.
Search: Posts Made By: pingu
Forum: Bioinformatics 02-21-2016, 11:38 PM
Replies: 1
orf
Views: 523
Posted By pingu
orf

Hello!
I would like to remove the dubious ORFs in my SAM file. How can I do it? Is there an option in Ensemble Api perl that allow me to not include the dubious ORF? Or another way?
Thank you in...
Forum: Bioinformatics 12-18-2015, 05:32 AM
Replies: 1
Views: 648
Posted By pingu
file bed

Hello! I have a manifest file from Illumina and I would like to extract bed file. In the manifest file the targets have a strand + o - and in the file bed I would like to specify they, I see that it...
Forum: Bioinformatics 11-20-2015, 06:16 AM
Replies: 7
Views: 699
Posted By pingu
I would like to find variants, in a diagnostic...

I would like to find variants, in a diagnostic sector (I am working in a hospital).
Forum: Bioinformatics 11-20-2015, 05:57 AM
Replies: 7
Views: 699
Posted By pingu
Thank very much for your response. I am working...

Thank very much for your response. I am working with DNA, in particular with amplicons for BRCA1 and BRCA2, and I have the reference sequence (brca1 and brca2) but I think that it is better to align...
Forum: Bioinformatics 11-20-2015, 05:26 AM
Replies: 7
Views: 699
Posted By pingu
Alignment reads

Hello!
Do you suggest to align reads against whole genome or only chromosome?
I remembered that I have read that it is better to use whole genome (but I do not find the paper, if there is a paper...
Forum: Bioinformatics 11-15-2015, 05:58 AM
Replies: 1
Views: 880
Posted By pingu
Barcode splitter

Hello,
I am trying to use fastx barcode splitter, but I do not understand if with the option "partial matching " I can allow indel inside the read.
How does the tool count the mismatches? Does the...
Forum: Bioinformatics 11-03-2015, 01:09 AM
Replies: 4
Views: 905
Posted By pingu
I find the problem, I made a mistake, The tabs...

I find the problem, I made a mistake, The tabs are wrong.
Anyway thank you!!
Forum: Bioinformatics 11-03-2015, 12:54 AM
Replies: 4
Views: 905
Posted By pingu
Thank you very much for your help. I have used...

Thank you very much for your help. I have used perl to modify mi vcf (I have never used R )
For example, this is the original vcf:
##fileformat=VCFv4.1
##source=VarScan2...
Forum: Bioinformatics 11-02-2015, 04:53 PM
Replies: 4
Views: 905
Posted By pingu
snpsift

Hello!
I have used varscan in order to call my variants,now I would like filter they using frequency,
So I have tried snpsift, with this command:
java -jar SnpSift.jar filter "(GEN .FREQ>20)" ...
Forum: Bioinformatics 10-29-2015, 03:40 PM
Replies: 3
Views: 850
Posted By pingu
Thank you very much for your response. Yes, I...

Thank you very much for your response. Yes, I have bam and bed file. I would like calculate the coverage per amplicon. What it is the average coverage in bam? Is it important?

Thank you in advance
Forum: Bioinformatics 10-29-2015, 03:29 AM
Replies: 3
Views: 850
Posted By pingu
Coverage amplicon

Hello,
How can I calculated my coverage for amplicons?
Thank you very much in advance
Forum: Bioinformatics 10-27-2015, 12:00 AM
Replies: 3
Views: 766
Posted By pingu
Thank you very much for your response. I am...

Thank you very much for your response. I am implementing my pipeline in order to analyse BRCA1 and BRCA2. The initial length of the reads is about 300bp, I don't know distribution of insert size, how...
Forum: Bioinformatics 10-24-2015, 07:51 AM
Replies: 3
Views: 766
Posted By pingu
length reads after trimming

Hello!
I have to trim primers of my reads, after trimming are there a length of reads suggest? So I would understand if I have to discard short reads. My analysis is on DNA.
Thank you very much in...
Forum: Bioinformatics 10-19-2015, 03:45 AM
Replies: 4
Views: 1,205
Posted By pingu
Thank you very much for your precious help. You...

Thank you very much for your precious help. You are right, the deletion is T.
I have tried "bcftools norm" to normalize calls of my GATK vcf ( in particular I have used this command: ./bcftools...
Forum: Bioinformatics 10-18-2015, 02:51 PM
Replies: 4
Views: 1,205
Posted By pingu
Thank you very much for your help. But if I...

Thank you very much for your help.
But if I take the reference sequence from chr13:32900363-32900371 : CTTTTTTTA
I do not understand how is it possible that my vcf reports that in the 32900363 I...
Forum: Bioinformatics 10-17-2015, 01:18 PM
Replies: 4
Views: 1,205
Posted By pingu
gatk position indel

Hello,
I am implementing my pipeline for Roche 454 Junior and I have used GATK for called of variants.
I have compared my variants with Roche's variants and for BRCA1 my variants corresponded, but...
Forum: 454 Pyrosequencing 10-05-2015, 07:13 AM
Replies: 0
Views: 2,282
Posted By pingu
homopolymer, steps after alignment

Hello.
I am implementing my pipeline and I have to start the steps after alignment. I have see on GATK pipeline that I have to do local realignment (indel realignment) but the problem of 454 Roche...
Forum: The Pipeline 09-25-2015, 03:13 AM
Replies: 1
Views: 4,327
Posted By pingu
Length read

Hello!
I am using 454 Roche Junior and I would be trim my primers. How much it must be length a read for be accepted before both trimming and after?
Thank you in advance
Forum: Bioinformatics 09-24-2015, 05:09 AM
Replies: 5
Views: 1,332
Posted By pingu
Thank you for your response. I have tried use...

Thank you for your response. I have tried use that command. I think that probably the problem is in the structure of my file with adapter. Please could you write me an example of the structure? ...
Forum: Bioinformatics 09-23-2015, 04:51 AM
Replies: 5
Views: 1,332
Posted By pingu
Thank you for your response, yes I have tried...

Thank you for your response, yes I have tried also the anchored 5'-adapter removal option. If I use a single adapter Cutadapt trims, so I think that the problem is when I use a list of adapter...
Forum: Bioinformatics 09-23-2015, 03:18 AM
Replies: 5
Views: 1,332
Posted By pingu
Cutadapt, list of adapter

Hello,

I am using Cutadapt, but I have a problem: It doesn't find adapter, but with a banal research with function "find" in the file I find adapters, so I am sure that they are in my file.
...
Forum: Bioinformatics 09-19-2015, 09:25 AM
Replies: 3
Views: 972
Posted By pingu
Thank you for your help, I know the barcodes and...

Thank you for your help, I know the barcodes and they are at the of the reads (last 10bp)
For example, this read is not assigned:
@JBMBIZC01CKLPI...
Forum: Bioinformatics 09-19-2015, 01:45 AM
Replies: 3
Views: 972
Posted By pingu
Demultiplexing

Hello,
I have to demultiplex my fastq file, I have seen that about 200 reads are not assigned (total is 17000), there is a tool that can check barcode on 5' and 3'?
Thank you very much
Forum: 454 Pyrosequencing 09-15-2015, 05:08 AM
Replies: 3
Views: 2,623
Posted By pingu
Thank you very much for your response. I have...

Thank you very much for your response. I have another question: is it a problem if my amplicon is longer than final read and it is possibile that the end (3') of my read is incomplete?

Thank you...
Forum: 454 Pyrosequencing 09-14-2015, 08:04 AM
Replies: 3
Views: 2,623
Posted By pingu
SFF file - primers

Hello!
I am using 454 Roche Junior, I have few questions about reads of sff file.
I have splitted a SFF file into individual SFF file (according to their MIDs), I don't understand if I have to do...
Showing results 1 to 25 of 26

 


All times are GMT -8. The time now is 04:44 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO