SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 36
Search took 0.00 seconds.
Search: Posts Made By: gmarco
Forum: Bioinformatics 05-20-2015, 12:24 AM
Replies: 2
Views: 1,984
Posted By gmarco
I'm experiencing weird behavior in cufflinks when...

I'm experiencing weird behavior in cufflinks when using Picard tools FixMateInformation on *.bam produced by tophat2.

Using picard-tools-1.129 and cufflinks v2.2.1.

I'm not getting same results...
Forum: Bioinformatics 01-13-2015, 05:08 AM
Replies: 8
Views: 2,760
Posted By gmarco
You should use bcl2fastq from Illumina to...

You should use bcl2fastq from Illumina to demultiplex your data. Download and employ version according to the sequencing instrument used to obtain the data.
Forum: Bioinformatics 06-23-2014, 02:02 AM
Replies: 1
Views: 2,398
Posted By gmarco
I've got answer from Daniel Zerbino (creator of...

I've got answer from Daniel Zerbino (creator of Velvet). In case anyone else interested:

Velvet does not support ambiguous call, it just makes a majority call.
Forum: Bioinformatics 06-22-2014, 11:36 PM
Replies: 1
Views: 2,398
Posted By gmarco
Question Velvet assembler ambiguous calls

Hello,

I'm using Velvet assembler and I've a little doubt.
After reading Velvet documentation I know that one gap in output assembly is represented by minimum of 10 N's. And that the number of...
Forum: Ion Torrent 06-09-2014, 12:32 AM
Replies: 14
Views: 15,087
Posted By gmarco
I'm very happy seeing this topic has received...

I'm very happy seeing this topic has received many answers. I'm wiling to try all these tools.



Hello wolfpack do you have any ETA?

I expected very very very slow GATK UnifiedGenotyper...
Forum: Ion Torrent 03-25-2014, 06:01 AM
Replies: 14
Views: 15,087
Posted By gmarco
I'm using GATK as I do with Illumina data. I'm...

I'm using GATK as I do with Illumina data. I'm experiencing very slow variant calling process with UnifiedGenotyper.
Forum: Ion Torrent 03-25-2014, 04:07 AM
Replies: 14
Views: 15,087
Posted By gmarco
Question Variant Calling outside Torrent Suite and TVC

Hello,

After trying to build Torrent Suite 4 for weeks on a RedHat Linux without success (I got compiled programs but not working with my Linux Architecture), and exploring all the tools they...
Forum: Bioinformatics 11-18-2013, 01:35 AM
Replies: 5
Views: 2,535
Posted By gmarco
Totally agree. Next time I'll test with public...

Totally agree. Next time I'll test with public data so I can get better help.
Flexbar is processing reads atm, it seems that's ok. Anyways I'll report when process is done.

BC split went...
Forum: Bioinformatics 11-17-2013, 10:54 PM
Replies: 5
Views: 2,535
Posted By gmarco
I cannot send this data (it's private). But i'm...

I cannot send this data (it's private). But i'm gonna try with flexbar and skewer.
I'll report asap.
Forum: Bioinformatics 11-15-2013, 05:34 AM
Replies: 5
Views: 2,535
Posted By gmarco
Question Illumina - Paired End Barcode Split + Mip trimmer

Hello,

I've received a data set of old Illumina PE data. (R1, R2, R3).

Paired end files are R1 and R3.

I've split R1 and R3 into sample barcodes with fastx_barcode_splitter.
Then I...
Forum: Bioinformatics 11-06-2013, 02:12 AM
Replies: 3
Views: 1,577
Posted By gmarco
Then I guess 1000genomes reference for phase 2...

Then I guess 1000genomes reference for phase 2 is:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz

Maybe I miss explained myself. I...
Forum: Bioinformatics 11-05-2013, 11:53 PM
Replies: 3
Views: 1,577
Posted By gmarco
If there's no human reference coming from 1000...

If there's no human reference coming from 1000 genomes data, is there any other alternatives to standard hg19?
Forum: Bioinformatics 11-05-2013, 06:34 AM
Replies: 3
Views: 1,577
Posted By gmarco
Question 1000 genomes human reference

Hello,

I'm using hg19.

As you may know when you perform variant calling, reference variation allele may be biased due to the human reference we use (it's very uncommon but it does happen).

I...
Forum: Bioinformatics 10-03-2013, 11:32 PM
Replies: 0
Views: 1,800
Posted By gmarco
Unhappy Nextera Expanded Exome BWA aln

Hello,

I'm trying to align Nextera Expanded Exome (62Mb) samples from HiSeq 2000 (Paired end ~99bp insert size) with BWA aln.

I'm having some troubles. Calculate SA coordinate seems to take a...
Forum: Bioinformatics 09-30-2013, 06:14 AM
Replies: 3
Views: 3,595
Posted By gmarco
Indeed it accepts -L option for specify...

Indeed it accepts -L option for specify intervals. But I want per gene coverage report. That's why I need to generate RefSeq file from BED.
Forum: Bioinformatics 09-30-2013, 02:52 AM
Replies: 3
Views: 3,595
Posted By gmarco
Question BED to RefSeq gene format

Hello,

I would like to convert a BED interval file to RefSeq format. I need this to use it among with GATK DepthOfCoverage.

I've been trying loading custom track on UCSC....
Forum: Bioinformatics 09-25-2013, 07:53 AM
Replies: 6
Views: 3,434
Posted By gmarco
Loading fasta... never ends.

Loading fasta... never ends.
Forum: Bioinformatics 09-24-2013, 10:54 PM
Replies: 6
Views: 3,434
Posted By gmarco
Question Merging two bacteria de novo assemblies into one

Hello,

I'm trying to merge a bacterial genome assembly done by myself with Velvet with another I got from partner.

Both assemblies data come from Illumina MiSeq platform (Paired End).

I've a...
Forum: Bioinformatics 09-23-2013, 11:54 PM
Replies: 2
Views: 2,889
Posted By gmarco
Seem to be a directory permission issue. CISA...

Seem to be a directory permission issue. CISA doesn't like NFS mount directories..
Forum: Bioinformatics 09-20-2013, 12:31 AM
Replies: 2
Views: 2,889
Posted By gmarco
Question CISA assembly contig integrator error

Hello,

I'm trying to use CISA to merge and optimize two de novo bacterial assemblies.
Process seems to work fine until the very last step. I'm getting this error:

Traceback (most recent call...
Forum: Bioinformatics 09-13-2013, 06:59 AM
Replies: 7
Views: 5,959
Posted By gmarco
I suppose pMap will work flawlessly on a Rocks...

I suppose pMap will work flawlessly on a Rocks cluster based on SGE right?
It supports bowtie, does it also supports bowtie2?

Thanks.
Forum: Bioinformatics 09-13-2013, 06:23 AM
Replies: 6
Views: 10,369
Posted By gmarco
I'm also interested on this information.

I'm also interested on this information.
Forum: Bioinformatics 07-22-2013, 01:42 AM
Replies: 6
Views: 7,590
Posted By gmarco
Hello Heisman, I'm trying sed command with...

Hello Heisman,

I'm trying sed command with no success:

sed -e 's,chrX,chr23,' -e 's,chrY,chr24' input.bed
sed: -e expression #2, char 12: unterminated `s' command

Fixed missing a comma...
Forum: Bioinformatics 07-19-2013, 05:17 AM
Replies: 6
Views: 7,590
Posted By gmarco
Don't you have to also remove "chr" from line...

Don't you have to also remove "chr" from line start to make the sort work?
Forum: Bioinformatics 07-19-2013, 04:57 AM
Replies: 6
Views: 7,590
Posted By gmarco
Unhappy Sort bed file by chr order and not lexicographically

I've been trying to sort a bed file with bedtools and bedops.

Both seem to sort the bed file lexicographically.

That means if my input test file is:

input:

chr1 10 30
chr2 30 10
Showing results 1 to 25 of 36

 


All times are GMT -8. The time now is 01:07 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO