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Forum: Epigenetics 09-27-2014, 10:18 PM
Replies: 3
Views: 2,115
Posted By volks
most CpGs in the genome are either unmethylated...

most CpGs in the genome are either unmethylated or methylated on both strands (CG is a palindromic sequence). any hemi-methylated CpGs are quickly methylated on both strands by DNMT1 (that is what is...
Forum: Bioinformatics 08-26-2014, 12:27 AM
Replies: 3
Views: 3,082
Posted By volks
you can use igvtools count --strands first for...

you can use igvtools count --strands first for creating a wig file that contains columns for both strands. subsequently use cut/awk and wigToBigWig.
Forum: Bioinformatics 05-15-2014, 03:14 PM
Replies: 13
Views: 2,156
Posted By volks
not sure if this is the question .. for illumina...

not sure if this is the question .. for illumina sequencing they actually both come from the same strand, just one of them shows the reverse complement (have a look at the details of the protocol)....
Forum: Bioinformatics 05-01-2014, 03:37 AM
Replies: 5
Views: 1,167
Posted By volks
i quite like xargs: ls -1 *fq | cut -d _ -f 1 |...

i quite like xargs:
ls -1 *fq | cut -d _ -f 1 | sort | uniq | xargs -I '{}' -P 4 sh -c "echo processing '{}'; fastq-join '{}'_r1.fq '{}'_r2.fq -o '{}'_merged.fq"
.. will run four commands in...
Forum: Bioinformatics 12-18-2013, 10:48 PM
Replies: 8
Views: 6,454
Posted By volks
what is the benefit of merging the fastq files?...

what is the benefit of merging the fastq files? you could merge bam files, e.g. using Picard MergeSamFiles or MarkDuplicates (if required, can be performed in a single step). then you could remove...
Forum: Bioinformatics 12-05-2013, 12:59 AM
Replies: 13
Views: 5,685
Posted By volks
if there are only female samples in the whole...

if there are only female samples in the whole study then i agree. otherwise the increased accuracy, which you couldnt achieve in male samples, might lead to false positive results?

so ENCODE...
Forum: Bioinformatics 12-05-2013, 12:36 AM
Replies: 13
Views: 5,685
Posted By volks
you would probably also create bias on other...

you would probably also create bias on other chromosomes, e.g. reads then mapping uniquely to chrX ..
Forum: Bioinformatics 12-05-2013, 12:35 AM
Replies: 13
Views: 5,685
Posted By volks
i still dont understand. why not just merge the...

i still dont understand. why not just merge the files as they are? why the reheader?

if the biological replicates are of different gender, maybe it would be best to exclude all reads mapping to...
Forum: Bioinformatics 12-02-2013, 09:43 AM
Replies: 13
Views: 5,685
Posted By volks
i see the need to account for gender in...

i see the need to account for gender in downstream analysis, but for what kind of data would it make a difference for the alignment (to include/not include chrY)?
Forum: Bioinformatics 11-29-2013, 12:39 AM
Replies: 1
Views: 1,179
Posted By volks
looks good to me. ...

looks good to me.

http://samtools.sourceforge.net/SAMv1.pdf
Forum: Bioinformatics 10-25-2013, 05:34 AM
Replies: 2
Views: 2,325
Posted By volks
i assume you are using pysam .. query and qqual...

i assume you are using pysam .. query and qqual will give you sequence and quality scores excluding softclipped bases.
...
Forum: Bioinformatics 07-18-2013, 10:18 AM
Replies: 6
Views: 1,645
Posted By volks
you will not have the exact same results. the...

you will not have the exact same results. the likelihood that will affect your conclusion is pretty low, it also depends on the question.
Forum: Bioinformatics 06-24-2013, 06:18 AM
Replies: 2
Views: 1,400
Posted By volks
that is the problem.

that is the problem.
Forum: Bioinformatics 02-26-2013, 02:38 AM
Replies: 8
Views: 2,079
Posted By volks
what is wrong with FASTA?

what is wrong with FASTA?
Forum: Bioinformatics 02-18-2013, 03:50 AM
Replies: 218
Views: 139,433
Posted By volks
i also like STAR a lot. so much simpler and...

i also like STAR a lot. so much simpler and faster than other tools around.

could you give an example how to use gzipped input files (--readFilesCommand)? i cannot get it to work.

thanks!
Forum: Bioinformatics 02-13-2013, 05:50 AM
Replies: 6
Views: 14,396
Posted By volks
i dont think realigning without certain parts of...

i dont think realigning without certain parts of the reference is a good idea, because some reads will instead be mapping elsewhere in the genome.

you could also use awk to filter:
samtools view...
Forum: Bioinformatics 01-13-2013, 03:52 AM
Replies: 15
Views: 3,187
Posted By volks
if you run it on default it will tell you what...

if you run it on default it will tell you what the number of mismatches are for various read lenghts. just double that.

i dont see why you should turn off seeding, and i am not sure if setting -l...
Forum: Bioinformatics 01-13-2013, 03:23 AM
Replies: 15
Views: 3,187
Posted By volks
defaults are given in brackets []. for starters...

defaults are given in brackets [].
for starters i would disable gapped alignment (-o 0), keep the seed at length and two mismatches (-l 32, -k 2) and try various different overall mismatches (e.g....
Forum: Bioinformatics 01-13-2013, 03:08 AM
Replies: 15
Views: 3,187
Posted By volks
if you are certain that BWA is your only option...

if you are certain that BWA is your only option ..
the parameters are pretty clear:

Options: -n NUM max #diff (int) or missing prob under 0.02 err rate (float) [0.04]
-o INT ...
Forum: General 01-13-2013, 02:56 AM
Replies: 7
Views: 1,753
Posted By volks
i am not sure of this. why wouldnt it? ...

i am not sure of this. why wouldnt it?

anyway, depending on your alignment file size you could also consider running a unix diff on the original and samtools-rmdup'ed SAM file.
Forum: Bioinformatics 01-13-2013, 02:47 AM
Replies: 15
Views: 3,187
Posted By volks
are you aligning against a transcript database?...

are you aligning against a transcript database? if not, you might consider using a splice aware aligner like tophat or star:
http://tophat.cbcb.umd.edu/
http://code.google.com/p/rna-star/
Forum: General 01-03-2013, 05:06 AM
Replies: 7
Views: 1,753
Posted By volks
try picard MarkDuplicates and then using samtools...

try picard MarkDuplicates and then using samtools view -f 1024
Forum: Bioinformatics 01-03-2013, 04:59 AM
Replies: 4
Views: 1,694
Posted By volks
fastaFromBed from bedtools?

fastaFromBed from bedtools?
Forum: Bioinformatics 03-20-2012, 02:39 AM
Replies: 3
Views: 2,144
Posted By volks
please define ridiculous size. for whole-genome...

please define ridiculous size. for whole-genome sequencing of human samples you can easily end up with alignments >100Gb.
Forum: Bioinformatics 03-20-2012, 01:05 AM
Replies: 4
Views: 1,610
Posted By volks
yes, from bam to bam (-b). there is hardly ever...

yes, from bam to bam (-b).
there is hardly ever a reason to write a sam file to disk.
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