User: Yaseen Ladak
Yaseen Ladak • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- United Kingdom, London, Imperial College London
- Last seen:
- 2 years, 7 months ago
- Joined:
- 3 years, 8 months ago
- Email:
- y***********@gmail.com
Posts by Yaseen Ladak
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C: Accessor methods for Bio::SeqIO
... Thank you very much. Thats very helpfiul. ...
written 2.7 years ago by
Yaseen Ladak • 20
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Comment:
C: Accessor methods for Bio::SeqIO
... Thank you for editing. What is 101010 button and is it for code formatting? When can I use that? ...
written 2.7 years ago by
Yaseen Ladak • 20
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... Hello All,
I need some help.
I am trying to use Bio::SeqIO. How can I know what accessor functions does this module have like for example:
my $seqin = Bio::SeqIO->new(-file => "myfile.fa", -format => "fasta");
my $seqout = Bio::SeqIO->new(-file => ">myfile_100.fa" ...
written 2.7 years ago by
Yaseen Ladak • 20
• updated
2.7 years ago by
WouterDeCoster ♦ 40k
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... Thank you. Thats very helpful :) ...
written 2.7 years ago by
Yaseen Ladak • 20
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... Thanks, I would be more careful next time. ...
written 2.7 years ago by
Yaseen Ladak • 20
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... Dear All,
I would really appreciate some help.
I have a aligned BAM file which is sorted. This file was obtained from paired end sequencing. I am trying to find the raw counts which fall in the regions mentioned in the GTF.
The GTF is below:
*********************************
1dh10b ena e ...
written 2.7 years ago by
Yaseen Ladak • 20
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... Thanks but genes.attr_table does not give me the count. I want to have the counts with the gene id and gene names. ...
written 3.2 years ago by
Yaseen Ladak • 20
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... Thank you very much really grateful for your support and this forum! ...
written 3.2 years ago by
Yaseen Ladak • 20
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... Hi All,
I need a little help, the output of cuffnorm from the genes.fpkm_table file is as follows:
tracking_id q1_0 q2_0
ECDH10B_0001 0 0
ECDH10B_0002 12.7841 26.1493
ECDH10B_0003 20.8691 21.9675
ECDH10B_0004 25.1604 47.0917
How can I include the gene name in the output file in addition to the ge ...
written 3.2 years ago by
Yaseen Ladak • 20
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... Hello All,
I am trying to use cuffnorm to normalise the counts. However, I am giving inputs as BAM files and I have the GTF obtained from ensembl. Do I need to use cufflinks as the first step to generate the GTF to be used with Cuffnorm or can I use the GTF that I have obtained from emnsebl for the ...
written 3.2 years ago by
Yaseen Ladak • 20
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