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User: Yaseen Ladak

gravatar for Yaseen Ladak
Yaseen Ladak • 30
Reputation:
30
Status:
New User
Location:
United Kingdom, London, Imperial College London
Last seen:
4 years, 1 month ago
Joined:
5 years, 2 months ago
Email:
y***********@gmail.com

Posts by Yaseen Ladak

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Accessor methods for Bio::SeqIO
... Thank you very much. Thats very helpfiul. ...
written 4.2 years ago by Yaseen Ladak • 30
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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 4.2 years ago by Yaseen Ladak • 30
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Accessor methods for Bio::SeqIO
... 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" ...
fasta sequence bio perl sequencing written 4.2 years ago by Yaseen Ladak • 30 • updated 4.2 years ago by WouterDeCoster ♦ 45k
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Comment: C: Raw counts - FeatureCounts (Rsubread), HT Seq and BEdtools
... Thank you. Thats very helpful :) ...
written 4.2 years ago by Yaseen Ladak • 30
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Comment: A: Raw counts - FeatureCounts (Rsubread), HT Seq and BEdtools
... Thanks, I would be more careful next time. ...
written 4.2 years ago by Yaseen Ladak • 30
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Raw counts - FeatureCounts (Rsubread), HT Seq and BEdtools
... 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 ...
next-gen rna-seq written 4.2 years ago by Yaseen Ladak • 30
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Answer: A: Cuffnorm output files gives only geneid and not gene names in annotation
... 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 4.7 years ago by Yaseen Ladak • 30
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Answer: A: Cuffnorm for normalisatioin of counts
... Thank you very much really grateful for your support and this forum! ...
written 4.7 years ago by Yaseen Ladak • 30
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Cuffnorm output files gives only geneid and not gene names in annotation
... 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 ...
rna-seq written 4.7 years ago by Yaseen Ladak • 30
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Cuffnorm for normalisatioin of counts
... 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 ...
rna-seq written 4.7 years ago by Yaseen Ladak • 30

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