User: R
R • 10
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Posts by R
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C: unique list of promoters
... Currently, for some types of analysis like histone mark enrichment analysis , ...
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written 5.3 years ago by
R • 10
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... I have a very basic question. I would like to have unique list of promoters.
Let's say we have Refseq genes downloaded from Table browser (~54k).
If we extend the TSS with whatever kb up and down, how should we make the list unique? gene name or position?
e.g.
chr1 6052357 6161253 NM_0011998 ...
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C: mapping PE or SE?
... Thanks! I already mapped as PE. Do you think is better to map it again as SE or taking one mate from PE-mapped file is also fine?
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written 5.3 years ago by
R • 10
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... Hi,
I want to compare two data sets, one of them is SE and the other one is PE.
What's the difference if I map the PE data set and after mapping take mate1 and do further analysis or it is better to take one mate and map it as SE at the beginning ?
PS: I did both and I got equally the same amount ...
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... Hi I would like to separate 1/2 mates of a paired-end bam file.
To see first mate:
samtools view -F 0x40 in.bam
To see second mate:
samtools view -F 0x80 in.bam
but it returns the following as first mate (0x40):
H0544AFXX:1:11101:8739:1038 163 chr3 17908775 3 1S74M = 17909029 330 ...
and f ...
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... Does "my $db = Bio::DB::Fasta->new($file_fasta);" automatically write the index file into the current dir or I am doing sth wrong. When I ran the first script I saw the hg19.fa.index created in the curent dir!!
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written 5.5 years ago by
R • 10
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... I would like to reload a pre-index file in perl which has been previously indexed as following:
./first_script.pl hg19.fa
use Bio::DB::Fasta;
my $db = Bio::DB::Fasta->new($file_fasta);
...
in an another script I would like to re-load the existing indexed file.
./script.pl hg19.fa.index inp ...
written 5.5 years ago by
R • 10
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... linux-3.17.8-gentoo-r1
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written 5.5 years ago by
R • 10
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... I'v tried that BUT Couldn't open - , No such file or directory ;((((((
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written 5.5 years ago by
R • 10
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... I also tried stdin. I did not work
...
written 5.5 years ago by
R • 10
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