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Forum: Bioinformatics 07-04-2013, 04:57 AM
Replies: 3
Views: 1,834
Posted By hanshart
20 bases sounds ok for mouse, but even then I...

20 bases sounds ok for mouse, but even then I would stick to "uniquely" mappable reads, as even for 20bp reads for such a large genome like mm there will be many reads that could be mapped to many...
Forum: Bioinformatics 07-02-2013, 10:04 AM
Replies: 7
Views: 4,437
Posted By hanshart
An example for Bowtie: 1. Determine the...

An example for Bowtie:

1. Determine the sequences of your contaminants and write them to a FASTA file like


(or directly use an available FASTA describing your contaminants)

2. Build a...
Forum: Bioinformatics 07-01-2013, 07:45 AM
Replies: 4
Views: 4,866
Posted By hanshart
Thank you maubp. About the different sorting in...

Thank you maubp.
About the different sorting in version 0.1.19 in contrast to version 0.1.18:
I'm quite sure that in version 0.1.19 reads beginning at the same position are now sorted by strand...
Forum: Genomic Resequencing 06-30-2013, 04:32 AM
Replies: 40
Views: 38,398
Posted By hanshart
Hi Vishnu, The indexing itself is not that...

Hi Vishnu,
The indexing itself is not that important for you, it is just an algorithm to store your reference in a nice data structure. Every aligner uses it's own indexing strategy based on the...
Forum: Bioinformatics 06-29-2013, 12:45 PM
Replies: 4
Views: 4,866
Posted By hanshart
Thank you for your answer Heisman, actually I...

Thank you for your answer Heisman,
actually I was wrong.
There is no difference in the way of sorting (either with or without the pipe). Sorry for the confusion, I edited my first post.

The...
Forum: Bioinformatics 06-29-2013, 10:09 AM
Replies: 4
Views: 4,866
Posted By hanshart
samtools sort

Hi,

I just installed the latest samtools (0.1.19-44428cd) and now I have an issue with my SAM->BAM->BAM_Sorted Pipeline using the Linux pipe. In samtools version 0.1.18 (r982:295) the following...
Forum: Bioinformatics 06-24-2013, 08:17 PM
Replies: 7
Views: 4,437
Posted By hanshart
Hi Guigra, without deeply understanding of your...

Hi Guigra,
without deeply understanding of your problem: If you know the type of contaminant you can always build an index of its corresponding genome/identifier sequences and map all reads to this...
Forum: Bioinformatics 06-24-2013, 08:09 PM
Replies: 5
Views: 1,445
Posted By hanshart
Hi annavilborg, you can additionally pipe your...

Hi annavilborg,
you can additionally pipe your sorted output to awk to get only those lines (genes) with read count above your threshold. Figure out which column (field) stores the read counts and...
Forum: Bioinformatics 06-24-2013, 01:54 AM
Replies: 36
Views: 18,832
Posted By hanshart
He just said that for read counting issues (like...

He just said that for read counting issues (like differential expression analyses) the filtering based on annotation descriptors would be easier than to filter prior to the alignment (map against...
Forum: Bioinformatics 06-21-2013, 01:29 AM
Replies: 2
Views: 915
Posted By hanshart
Hi evepy88, In Linux you can use awk to...

Hi evepy88,
In Linux you can use awk to rearrange your fields
The following code will do the job:
awk 'BEGIN{FS="[|>]"}{print "> "$3$2}'

FS="[|>]" determines the field seperators to be "|" or...
Forum: Bioinformatics 05-17-2013, 04:14 AM
Replies: 1
Views: 2,770
Posted By hanshart
ENSEMBL biotype tRNA and non-coding RNA

Hello, I have two questions concerning the ENSEMBL annotation files (GTFs for human, mouse).

1. Can anyone explain to me why there is no gene_biotype "tRNA" (but "rRNA","Mt_rRNA", "Mt_tRNA")...
Forum: Bioinformatics 03-22-2013, 02:15 AM
Replies: 5
Views: 3,732
Posted By hanshart
It's possible to use fqgrep...

It's possible to use fqgrep (https://github.com/indraniel/fqgrep) for the approximative sequence search.
Forum: Introductions 12-20-2012, 04:12 AM
Replies: 13
Views: 12,495
Posted By hanshart
This is ok. It takes some time and after...

This is ok. It takes some time and after finishing the process the temporary files are deleted.
Forum: Bioinformatics 10-25-2012, 11:13 PM
Replies: 0
Views: 1,049
Posted By hanshart
Bowtie2 / Bowtie 2 multiseed strategy

Hi everyone,
I have a question about Bowtie2's multiseeding. How is Bowtie2 handling seeds that overlap the end of the read (because they are longer than the read or because of the...
Forum: Bioinformatics 10-07-2012, 11:34 AM
Replies: 3
Views: 1,118
Posted By hanshart
Its rRNA. But many sequences occur more than...

Its rRNA. But many sequences occur more than once. Sequences that occur many times could be identified this way and filtered out in the next experiments. That's the idea behind the question.
Forum: Bioinformatics 09-28-2012, 01:45 AM
Replies: 3
Views: 1,118
Posted By hanshart
assemble sequences to

Hi,
FASTQC can provide duplicate sequences during quality control of fastq data. But not all of them are really "unique" (=some of them are only partial sequences of a larger parental sequence (e.g....
Forum: Bioinformatics 03-15-2012, 07:52 AM
Replies: 0
Views: 1,583
Posted By hanshart
Bowtie2 / Bowtie 2 gapped alignment

this thread can be deleted
Forum: Bioinformatics 03-14-2012, 11:11 AM
Replies: 0
Views: 729
Posted By hanshart
Bowtie depth-first vs. best-first

Hi

Can anyone explain the difference between the depth-first backtracking approach and the --best (best-first) approach in Bowtie? Or in other words, what is depth-first doing and why does it not...
Forum: RNA Sequencing 03-07-2012, 04:29 AM
Replies: 10
Views: 2,661
Posted By hanshart
Thank you Simon for this precise answer. I never...

Thank you Simon for this precise answer. I never have seen this fact (don't ask me why). I totally agree with you and should ask my advisor how to deal with this problem :)
Forum: RNA Sequencing 03-07-2012, 03:56 AM
Replies: 10
Views: 2,661
Posted By hanshart
@ Jean 1.) I also observed the hiccups you...

@ Jean
1.) I also observed the hiccups you mentioned in cufflinks. DESeq didn't show any problems with the configuration I stated above.

4.) As you said, I can only observe the "big obvious...
Forum: RNA Sequencing 03-07-2012, 03:44 AM
Replies: 10
Views: 2,661
Posted By hanshart
Thank you all for your answers and sorry for the...

Thank you all for your answers and sorry for the ambiguous explanations. I will try to explain it more detailed now.

I have 16 different samples from 16 different human tissues (e.g. liver, brain,...
Forum: RNA Sequencing 03-04-2012, 11:39 PM
Replies: 10
Views: 2,661
Posted By hanshart
Can anyone help me with this, please?

Can anyone help me with this, please?
Forum: RNA Sequencing 02-25-2012, 07:02 AM
Replies: 10
Views: 2,661
Posted By hanshart
DESeq questions

Hello,

I have 16 samples from 16 different human tissues (say "A","B",...,"P"), so no biological replicates (75bp single end reads). I want to study the expression levels of a specific group of...
Forum: General 01-04-2012, 03:35 AM
Replies: 1
Views: 1,797
Posted By hanshart
Hi, you can simply redirect the output to a...

Hi,
you can simply redirect the output to a file using

after the bowtie call

or you can use the pipe (|) and shell commands like grep, head, tail, awk etc. to filter the output. e.g.
Forum: Bioinformatics 12-13-2011, 10:36 PM
Replies: 4
Views: 2,494
Posted By hanshart
Hi, From...

Hi,

From http://www.broadinstitute.org/software/igv/BAM:


You can use samtools for sorting and indexing the BAM file using the commands
samtools sort aln.bam aln.sorted
samtools index...
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