User: R

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R10
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3 years, 1 month ago
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6 years, 3 months ago
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Posts by R

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Comment: C: unique list of promoters
... Currently, for some types of analysis like histone mark enrichment analysis , ... ...
written 5.3 years ago by R10
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unique list of promoters
... 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 ...
gene chip-seq written 5.3 years ago by R10 • updated 5.3 years ago by RamRS30k
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Comment: 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? ...
written 5.3 years ago by R10
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mapping PE or SE?
... 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 ...
chip-seq written 5.3 years ago by R10 • updated 5.3 years ago by Fidel1.9k
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first and second mate reports by samtools 0x40 and 0x60 FLAGs
... 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 ...
alignment rna-seq sequencing written 5.4 years ago by R10 • updated 5.4 years ago by pengchy430
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Comment: C: Can't call method "index_file" on an undefined value at script.pl line ...
... 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!! ...
written 5.5 years ago by R10
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Can't call method "index_file" on an undefined value at script.pl line ...
... 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 ...
perl written 5.5 years ago by R10
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Comment: C: get an error "Expecting at least 3 words line 1 of /dev/stdin got 1" making bigB
... linux-3.17.8-gentoo-r1 ...
written 5.5 years ago by R10
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Comment: C: get an error "Expecting at least 3 words line 1 of /dev/stdin got 1" making bigB
... I'v tried that BUT Couldn't open - , No such file or directory  ;(((((( ...
written 5.5 years ago by R10
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Comment: C: get an error "Expecting at least 3 words line 1 of /dev/stdin got 1" making bigB
... I also tried stdin. I did not work ...
written 5.5 years ago by R10

Latest awards to R

Popular Question 4.9 years ago, created a question with more than 1,000 views. For get an error "Expecting at least 3 words line 1 of /dev/stdin got 1" making bigBed
Popular Question 4.9 years ago, created a question with more than 1,000 views. For counting reads over repeats
Popular Question 4.9 years ago, created a question with more than 1,000 views. For which kind of gene_biotype should we usaully remove?
Popular Question 4.9 years ago, created a question with more than 1,000 views. For how to use bed file as a input for htseq-count
Popular Question 4.9 years ago, created a question with more than 1,000 views. For p-value or adjusted p-value?

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