SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 107
Search took 0.02 seconds.
Search: Posts Made By: dietmar13
Forum: Bioinformatics 12-16-2016, 12:35 AM
Replies: 217
Views: 109,114
Posted By dietmar13
dear alex, or other star experts

which parameters should I set to get ALL non-canonical (i.e. back) spliced reads in the unmapped sam file. I want call circular RNAs with these reads.

I have 50 bp paired-end unstranded RNA-seq...
Forum: Bioinformatics 05-06-2015, 05:48 AM
Replies: 6
Views: 729
Posted By dietmar13
@GenoMax

I didn't try 1 because 2 works. in 1 trimming will be made twice (would be a real waste of resources)...
Forum: Bioinformatics 05-05-2015, 11:16 PM
Replies: 6
Views: 729
Posted By dietmar13
probably,

but in the first case, bash uses (probably) named pipes internally, in the other case I set and use the named pipes (and i think this is meant with "named pipes" in bash)...
Forum: Bioinformatics 05-05-2015, 05:41 AM
Replies: 6
Views: 729
Posted By dietmar13
to answer my own question: it works...

it works as follows:



dietmar
Forum: Bioinformatics 05-05-2015, 02:06 AM
Replies: 6
Views: 729
Posted By dietmar13
BBduk in process substitution or with named pipes?

hello (brian),

would it be possible to use bbduk as process substituion for mapping, like this.

mapper read1 <(bbduk.sh in1=R1.fastq.gz in2=R2.fastq.gz out1=stdout.fq out2=NULL ref=ref.fa.gz...
Forum: Bioinformatics 04-29-2015, 10:48 PM
Replies: 1
Views: 874
Posted By dietmar13
BBMap for BitSeq

Hello,

I want use BBmap for estimating transcript expression level from RNA-seq reads. Mapped will be against transcripts, not the genome.

The Manual for BitSeq uses Bowtie with following...
Forum: Bioinformatics 03-30-2015, 12:40 AM
Replies: 217
Views: 109,114
Posted By dietmar13
2-pass speed about 7 M/hr

hello,

is it possible that mapping speed for the 2nd pass decreases to 7 M/hr if 900.000 new splice sites and a comprehensive gene model (gencode v19) were used for index generation.
first pass...
Forum: Bioinformatics 06-24-2014, 07:12 AM
Replies: 2
Views: 1,617
Posted By dietmar13
thank you brian, that is was i thought...

thank you brian,

that is was i thought...
Forum: Bioinformatics 06-22-2014, 11:14 PM
Replies: 2
Views: 1,617
Posted By dietmar13
HaloPlex for very rare SNV detection (brian: ecc.sh will help?)

hello all,

has someone used HaloPlex data (agilent, similar SureSelect) for detection of very rare mutations (down to 0.5%)?

this means very deep data (up to few 100k coverage) for very small...
Forum: Bioinformatics 04-09-2014, 11:27 PM
Replies: 14
Views: 4,024
Posted By dietmar13
"Why do you want to detect extremely low abundant...

"Why do you want to detect extremely low abundant mutations?"

because i have a mixture of many non-cancer cells with (probably) only few cancer cells and want detect the latter using targeted...
Forum: Bioinformatics 02-15-2014, 04:04 PM
Replies: 3
Views: 1,200
Posted By dietmar13
new biostrings R-package ...

the new "biostrings" R-package needs some modifications of the R-script in the progs folder (attached).

and all sequences have to be RNA sequences (uU instead of tT).

using a large file of...
Forum: Bioinformatics 02-12-2014, 10:51 AM
Replies: 26
Views: 5,858
Posted By dietmar13
thank you,

sorting solved the problem.

dietmar
Forum: Bioinformatics 02-11-2014, 06:27 AM
Replies: 26
Views: 5,858
Posted By dietmar13
@luitpold

dear luitpold,

thank you!

but i always get this error:
testrealign.x: libs/memory.c:18: bl_realloc: Assertion `ptr != ((void *)0)' failed.
./testrealign_CoCa_CoNo.sh: line 11: 5078 Aborted ...
Forum: Bioinformatics 02-11-2014, 02:43 AM
Replies: 26
Views: 5,858
Posted By dietmar13
circular RNA

dear segemehl programmer,

which conditions are the best for finding back-spliced (circular) transcripts from 50 PE illumina reads.

i would run with following parameters:

./segemehl.x -t 20...
Forum: Bioinformatics 02-05-2014, 11:06 PM
Replies: 2
Views: 1,163
Posted By dietmar13
Agrep

agrep, a fuzzy grep version:
http://en.wikipedia.org/wiki/Agrep

best implemeted in TRE:
http://en.wikipedia.org/wiki/TRE_(computing)
Forum: Bioinformatics 01-23-2014, 11:06 AM
Replies: 24
Views: 7,676
Posted By dietmar13
Rum

why is RUM always neglected by comparing RNA-seq mappers?
In my hands RUM outperforms other pipelines, e.g. tophat, in sensitivity, especially for spliced reads...

RUM: RNA Seq Unified Mapper...
Forum: Bioinformatics 01-06-2014, 03:20 AM
Replies: 3
Views: 1,485
Posted By dietmar13
problem not solved

dear marco,

thank you, but the problem is the same.

what could be wrong with cap3?
file "vfs_dev.HKCI5a_gz.CSm.out.CS.fa.sim" is empty!

cap3 works on their example data set xyz...

OS:...
Forum: Bioinformatics 01-03-2014, 11:08 AM
Replies: 3
Views: 1,485
Posted By dietmar13
I got also an error, cap3 crashed...

hello,

the run finished, but cap3 crahed twice...
the CSm and .contigs-files are empty.

what could be wrong with cap3?

OS: Scientific Linux 6.3 (=RHEL 6.3), bwa 0.7.5a (problem?)
Forum: Bioinformatics 01-02-2014, 01:41 AM
Replies: 0
Views: 800
Posted By dietmar13
Annotation of small RNA seq data?

hi,

i have small RNA seq data from ~ 50 isolated tumor cell samples (~700 mio reads) and found at least 1282 new miRNAs (predicted by two independent methods and supported by at least 100 reads)...
Forum: Bioinformatics 12-20-2013, 10:00 AM
Replies: 0
Views: 689
Posted By dietmar13
RiboZero and polyA RNA seq data?

hello,

does someone know a publicly available data set where RiboZero and polyA RNA seq data were generated from the same samples (or at least the same biological tissues)?

best,

dietmar
Forum: Bioinformatics 12-13-2013, 11:18 PM
Replies: 14
Views: 4,024
Posted By dietmar13
thank you all for your suggestions

@bukowski,

we look at liquid biopsies from cancer patients and want identify tumor DNA among a large number of non-cancer cells...

I will look into MuTect and VarScan2 first...

best,
...
Forum: Bioinformatics 12-12-2013, 11:28 PM
Replies: 14
Views: 4,024
Posted By dietmar13
rare cancer mutation detection pipeline

hello,

what is the best analysis pipeline for rare (<1%) cancer mutation detection from targeted (bait hybridization enrichment) resequencing (illumina)?

GATK?

and who has the best bait...
Forum: Bioinformatics 11-12-2013, 09:25 AM
Replies: 4
Views: 1,016
Posted By dietmar13
yes, but

@leightonP

I know the KEGG homepage :) but I didn't find a download page...

@GenoMax

I thought there could be some collections around, downloaded before they got commercial,...
Forum: Bioinformatics 11-12-2013, 08:45 AM
Replies: 4
Views: 1,016
Posted By dietmar13
sus scrofa (pig) KEGG pathways: where to find...

hello,

does someone know where to download KEGG pathways (xml) for sus scrofa (pig) (or have them to share).

thank you,

dietmar
Forum: Bioinformatics 11-11-2013, 09:47 AM
Replies: 2
Views: 687
Posted By dietmar13
that's easy

echo -e "ID\tCK1\tCK2\t..." > file_with_header.count
cat file.count >> file_with_header.count

\t means tab

use spaces "ID CK1 CK2 ..." if you have only spaces between columns...
Showing results 1 to 25 of 107

 


All times are GMT -8. The time now is 01:41 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO