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Forum: Bioinformatics 03-06-2013, 07:45 AM
Replies: 5
Views: 1,492
Posted By Dethecor
Fasta file chromosome names

Hi, can you post the result of:

grep ">" ref_genome.fasta

You can get these segfaults without message when your fasta header lines have spaces in them.

Cheers,
Paul
Forum: Bioinformatics 06-16-2012, 02:01 AM
Replies: 39
Views: 13,262
Posted By Dethecor
Sort by position or name

Hi vyellapa,

if you run htseq-count on paired-end reads then you might want a .sam file sorted by name. Your Unix sort command does this (I hope it deals with the header properly), samtools sort...
Forum: Bioinformatics 06-13-2012, 05:36 AM
Replies: 39
Views: 13,262
Posted By Dethecor
pysam dependency

Hi all,

indeed certain functions in HTSeq depend on an installed pysam. We have changed this so that now this error is only raised if one actually tries to call one of these functions while not...
Forum: General 11-08-2011, 12:57 AM
Replies: 5
Views: 3,774
Posted By Dethecor
Example

Hi,

here a toy example, which you can just transfer to your data-set:


> data.frame(SomeValue=seq(0,2,0.4))
SomeValue
1 0.0
2 0.4
3 0.8
Forum: General 11-07-2011, 10:54 AM
Replies: 5
Views: 3,774
Posted By Dethecor
What about as.integer

If that is really the problem then applying as.integer to your columns should work (note that: as.integer(12.9) == 12)

Cheers,
Paul
Forum: Bioinformatics 07-07-2011, 07:00 AM
Replies: 8
Views: 3,608
Posted By Dethecor
CNVs with exome sequencing

I think that depends on what technology you use and what you want to do with your data, from what I understand one would use whole-exome sequencing primarily for SNP detection and maybe finding some...
Forum: Bioinformatics 07-07-2011, 06:03 AM
Replies: 8
Views: 3,608
Posted By Dethecor
Normalization

The kind of normalization I was thinking about is based on a property of the sequence and not relative to other samples.
For example for two samples A and B with read-counts rc_a and rc_b you would...
Forum: Bioinformatics 07-07-2011, 04:29 AM
Replies: 8
Views: 3,608
Posted By Dethecor
Depth of Coverage

Assuming that you have a reference genome for your organism you can still spot such things by looking at the depth-of-coverage. In this way you will be able to see regions where your sample had more...
Forum: Bioinformatics 05-23-2011, 05:03 AM
Replies: 5
Views: 11,412
Posted By Dethecor
bash scripts 4tw

Assuming you're running bash (otherwise the syntax might be slightly different):


for fn in *.sra
do
../bin64/fastq-dump $fn
done


This will take all *.sra files in the current directory...
Forum: Bioinformatics 05-18-2011, 07:50 AM
Replies: 3
Views: 6,120
Posted By Dethecor
Mappability

Hi Phillip,

this can be done with HTSeq, but it requires some expertise in programming python (or some time to learn some python).

For mappability I like to generate reads of the same length as...
Forum: Bioinformatics 05-18-2011, 06:10 AM
Replies: 3
Views: 6,120
Posted By Dethecor
Windowsize or binary?

Hi Phillip,

you should specify more what you want to see. %GC per position would be a track that just tells you for each position whether it is a G or C or not.
But you probably want to compute...
Forum: Bioinformatics 05-05-2011, 08:07 AM
Replies: 6
Views: 2,143
Posted By Dethecor
Hi, so I don't really use bowtie for...

Hi,

so I don't really use bowtie for alignment any more, last did so at least half a year back.

-m 1 should suppress reporting of reads with more than 1 alignment i.e. report only uniquely...
Forum: Bioinformatics 05-05-2011, 07:20 AM
Replies: 6
Views: 2,143
Posted By Dethecor
I personally don't use it, I tried it a couple of...

I personally don't use it, I tried it a couple of times though and think it's a very nice tool for automating your ngs pipeline.

When you use bowtie there is a field called "Bowtie settings to...
Forum: Bioinformatics 05-05-2011, 06:43 AM
Replies: 6
Views: 2,143
Posted By Dethecor
See the bowtie manual

From the bowtie manual (http://bowtie-bio.sourceforge.net/manual.shtml#example-4-default--k-1)


As you can see, this constitutes the default behaviour of bowtie and you can specify something else...
Forum: Bioinformatics 09-07-2010, 01:55 AM
Replies: 6
Views: 1,957
Posted By Dethecor
samtools view your_file.bam | awk ' { if( $1 ==...

samtools view your_file.bam | awk ' { if( $1 == "your_read_id" ){print $_} } '

assuming that with read_id you meant the sequence name.

You could also implement similar behavior in c / c++ by...
Forum: Bioinformatics 09-02-2010, 06:46 AM
Replies: 1
Views: 1,975
Posted By Dethecor
Align them unpaired

You could also try to shorten the reads to avoid overlapping of the pairs (which is probably the cause of the bad alignment).

So, I have not examined that in detail but I think it happens if the...
Forum: Bioinformatics 08-18-2010, 01:49 AM
Replies: 14
Views: 3,755
Posted By Dethecor
better resolution plz . . . can't see a damn...

better resolution plz . . . can't see a damn thing on those snapshots :/
Forum: Bioinformatics 08-13-2010, 01:43 AM
Replies: 12
Views: 4,007
Posted By Dethecor
Why gsmapper?

Hi all,

just a question that popped into my mind. (I normally use output from Illumina machines)

Why do you need to use this gsmapper tool instead of a standard SNP-calling pipeline like:
...
Forum: Bioinformatics 07-13-2010, 02:09 AM
Replies: 5
Views: 2,743
Posted By Dethecor
Set intersection

Now, I'm not an expert in (Bio-)Perl, but what you are doing seems to be somewhere in the time complexity of O( |all reads| * |aligned reads| ) with a lot of file connections being opened.
...
Forum: Epigenetics 07-09-2010, 07:01 AM
Replies: 31
Views: 13,454
Posted By Dethecor
Quality Scores

I have seen things like that a couple of times when the quality scores of the reads were in a different scale than the default setting from bowtie, for example the bowtie manual states:
...
Forum: Bioinformatics 07-09-2010, 04:06 AM
Replies: 2
Views: 2,259
Posted By Dethecor
Have a look at the samtools pileup format

See here: http://samtools.sourceforge.net/pileup.shtml

also, if you run samtools with the following command "samtools pileup -c -f <reference_sequence> in.bam" you will get for each position the...
Forum: Bioinformatics 07-07-2010, 06:24 AM
Replies: 4
Views: 4,326
Posted By Dethecor
Define "Compare"

Maybe if you could specify what you want to compare there would be a bigger chance that someone will provide more useful information.

To me it sounds like something you would do on your own with a...
Forum: RNA Sequencing 07-06-2010, 08:06 AM
Replies: 3
Views: 9,458
Posted By Dethecor
Short Read Archive

Hi,

you could try the Short Read Archive (http://www.ncbi.nlm.nih.gov/sra), although their datasets are normally in files of at least 500 Mb . . . you could just download some and then extract a...
Forum: 454 Pyrosequencing 05-31-2010, 04:23 AM
Replies: 3
Views: 2,545
Posted By Dethecor
Clipping Nucleotides that are artifacts of the sequencing process

Hi,

I had a similar situation when we used a process for the reverse transcription (in RNA-Seq) that would add a couple of G's at the 3'-End of some of the Reads.

For me simply clipping all...
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