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Forum: Bioinformatics 06-04-2015, 11:33 PM
Replies: 0
Views: 1,769
Posted By DNAjunk
VEP variation cache

Hi all

When running VEP with ensembl annoation files I get errors of the form "Could not find variation cache for Chromosome..."

I downloaded genome (ie. pao1, $name.fa) and annotation...
Forum: Bioinformatics 03-26-2015, 04:30 AM
Replies: 1
Views: 848
Posted By DNAjunk
Map Ionproton reads

Hi all

How to best align Ionproton RNASeq reads with gaps (spliced) to a reference genome?

TMAP does align those reads but not gapped, right?

I tried GSNAP and GMAP but they both crash at...
Forum: Bioinformatics 11-12-2014, 06:57 AM
Replies: 0
Views: 1,072
Posted By DNAjunk
VEP variant effect predictor

Hi all

How to output the html summary AND the plain text stats file when using Ensembl's variant effect predictor script (VEP) ?

There is the option "--stats_text" which "Generate a plain text...
Forum: Bioinformatics 03-03-2014, 10:36 PM
Replies: 2
Views: 1,633
Posted By DNAjunk
Thanks for the advices! I also got the...

Thanks for the advices!
I also got the information from the author of the program that one should use freebayes without the ogap program according to the freebayes manual.
Forum: Bioinformatics 03-02-2014, 11:40 PM
Replies: 2
Views: 1,633
Posted By DNAjunk
freebayes with ogap

Hi !

I am trying to use freeBayes for variant calling and run into problems with the example provided in the freeBayes package.

When I run the following pipeline given in the package, I get the...
Forum: Ion Torrent 04-03-2013, 03:41 AM
Replies: 2
Views: 1,566
Posted By DNAjunk
PS: It seems that the merged bam file is present...

PS: It seems that the merged bam file is present and correct and only the presentation of the alignment (rate in percentage and curve) is wrong in the torrent suite browser. Although the combine...
Forum: Ion Torrent 04-03-2013, 01:08 AM
Replies: 2
Views: 1,566
Posted By DNAjunk
Problem with Combine Alignments

Hi

We're using Ion Proton with the latest Torrent Suite (3.4.1).
When we would like to merge data from different runs belonging to the same project, then suddenly the alignment rate of the...
Forum: Bioinformatics 12-19-2012, 03:22 AM
Replies: 2
Views: 1,729
Posted By DNAjunk
Yes, it can and according to this publication it...

Yes, it can and according to this publication it performs well
http://www.ncbi.nlm.nih.gov/pubmed/23236450?dopt=Abstract
Forum: Bioinformatics 03-23-2012, 07:23 AM
Replies: 9
Views: 11,684
Posted By DNAjunk
Hi I did not proceed making my own sam/bam...

Hi

I did not proceed making my own sam/bam files.

As for 454 read-mapping, the latest 454 mapping software can create BAM files. Also, GMAP, which I often use, outputs alignments in SAM format.
Forum: 454 Pyrosequencing 07-20-2011, 12:38 AM
Replies: 2
Views: 1,620
Posted By DNAjunk
I have got the same problem with newbler version...

I have got the same problem with newbler version 2.6
I am using sff files of genomic paired-end reads as input (original sff files and split into smaller files) mapping to mammalian genome.
Forum: Bioinformatics 04-15-2011, 07:29 AM
Replies: 2
Views: 1,742
Posted By DNAjunk
Thanks, westerman for the script. I would...

Thanks, westerman for the script.

I would like to convert the mapped reads into nucleotides and at the same time correcting the invalid color changes by using the reference sequence according to...
Forum: Bioinformatics 04-08-2011, 01:03 PM
Replies: 2
Views: 1,742
Posted By DNAjunk
Bioscope Ma conversion (to base space)

Hi

Has anybody written a script/c program that converts mapped color space reads to base space reads by using Bioscope's (vs 1.3.1) mapping file *.ma and the reference fasta file?

I know this...
Forum: Bioinformatics 04-08-2011, 12:58 PM
Replies: 0
Views: 914
Posted By DNAjunk
Bioscope pairing pipeline

Hi

Does anybody know how to correctly use parameters in the BioScope 1.3.1 pairing pipeline?

I wanted to set

pairing.mark.duplicates.processors.per.node = 1

in the pairing.ini files,...
Forum: Bioinformatics 01-30-2011, 11:10 PM
Replies: 12
Views: 6,368
Posted By DNAjunk
Can newbler detect new splice variants ?

Can newbler detect new splice variants ?
Forum: Bioinformatics 01-27-2011, 06:26 AM
Replies: 12
Views: 6,368
Posted By DNAjunk
I have used the latest version. But Bowtie is...

I have used the latest version. But Bowtie is still not able to map to long 454 reads in the first mapping round. Surely, for the IUM (initially unmapped reads) which comprise the majority of the 454...
Forum: Bioinformatics 01-26-2011, 10:59 PM
Replies: 12
Views: 6,368
Posted By DNAjunk
Cool RNA-Seq: TopHat with Roche/454 reads

Hellow

I have got Roche/454 RNA-Seq reads from human samples.
It seems that TopHat/Cufflinks is one of the most used pipeline for analyzing RNA-Seq data, however, for short reads only (non-454...
Forum: Bioinformatics 01-14-2011, 12:27 AM
Replies: 1
Views: 1,813
Posted By DNAjunk
solved: the full length color-space-coded reads...

solved: the full length color-space-coded reads are present in the bam file with the attribute CS:Z:
Forum: Bioinformatics 01-12-2011, 07:07 AM
Replies: 3
Views: 1,602
Posted By DNAjunk
you could look it up in the 454ReadStatus.txt...

you could look it up in the 454ReadStatus.txt file or the ace file if it was generated.
Forum: Bioinformatics 01-12-2011, 07:05 AM
Replies: 1
Views: 2,508
Posted By DNAjunk
newbler ignores minimal read length

Hi

Iíve got a question that came up recently regarding the minimal read length in an assembly.

I have 454 and SOLiD reads (35-50 bases) combined and tried to assemble using the "minlen"-option...
Forum: Bioinformatics 01-12-2011, 07:01 AM
Replies: 1
Views: 1,813
Posted By DNAjunk
bioscope ma to bam conversion

Hello

I have got a question related to the ma2bam conversion.

Is it somehow possible the output the raw read sequence and its quality values in the bam file (i.e. 50 bases) and not only the...
Forum: Bioinformatics 11-19-2010, 06:55 AM
Replies: 1
Views: 2,300
Posted By DNAjunk
samtools pileup c-option changes read quality

Hi

I might be wrong but I got the impression that when using the c-option in the pileup process, then the read qualities are changed (near an indel, N's are placed also):
(I am using version...
Forum: Bioinformatics 09-08-2010, 05:04 AM
Replies: 9
Views: 11,684
Posted By DNAjunk
it is written in C programming language. ...

it is written in C programming language.

I've tried to convert ACE files via AMOS to SAM, but there were too many errors during conversion...
Forum: Bioinformatics 09-08-2010, 04:44 AM
Replies: 9
Views: 11,684
Posted By DNAjunk
I am using a in-house mapping program that works...

I am using a in-house mapping program that works fine, however it doesn't create BAM/SAM output (also gsMapper/newbler doesn't generate BAM/SAM, right?)
Forum: Bioinformatics 09-08-2010, 04:28 AM
Replies: 9
Views: 11,684
Posted By DNAjunk
Lightbulb How to create a SAM/BAM file from scratch

Hi
Does anybody have written a script or programme that creates a SAM or BAM file based on the following alignment information:

1) 454-reads
2) read qualtities
3) reference sequence(s)
4) read...
Forum: Bioinformatics 09-07-2010, 11:55 PM
Replies: 8
Views: 2,012
Posted By DNAjunk
KevinLam: How can one generate the file you...

KevinLam:
How can one generate the file you have posted previously?
I am using BioScope command line vs 1.2

# Generated by: CountSamPositionErrors(7_F3.csfasta.ma.bam)
# Version: Bioscope...
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