User: abdul.suboor123
abdul.suboor123 • 0
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Posts by abdul.suboor123
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... I want to extract miRNAs from RNA-Seq data sets, is it possible? please can anyone tell me the method? I have RNA-seq data of about 600 accessions, I want to extract miRNA sequences from them. ...
written 15 days ago by
abdul.suboor123 • 0
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... Brother #Hafiz.Talhamalik, If you have extracted the miRNAs from RNA-seq data, please mention here your pipeline, I will be really thankful. ...
written 15 days ago by
abdul.suboor123 • 0
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... Thanks for your reply, yeah actually, i was extracting specific rows @Bastien Herve , it works for me. ...
written 13 months ago by
abdul.suboor123 • 0
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... I have two small RNA matrix files, having almost 87% overlap. I want to extract those columns which are only specific to file 1 and specific to file 2, I am giving an example of my data:
File1.Sample 1:
AAAAAAACAAGGATCAACAAGACT 0.0835 0 0.2743 0.197 0.069 ...
written 13 months ago by
abdul.suboor123 • 0
• updated
13 months ago by
Bastien Hervé ♦ 4.9k
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Comment:
C: splicing QTL plot
... As per my understanding, I have performed the trans - eQTL for small RNA based on genes associated SNPs , where each chromosome has shown. I am providing you the code , hope you may find it helpful.
`rm(list=ls())
setwd("H:/Data/sRNA eQTL data/eQTL smallRNA related/RNA_data_results/17_6_17 ...
written 14 months ago by
abdul.suboor123 • 0
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... I am doing small RNA quantification, I have data of 338 lines (samples). Till now i have count the RPM values but I want to extract the reads with RPM value >= 0.6 , and appears more than 60 times in all lines. Please provide me any method or script to perform this step. Thanks.
data file is bed ...
written 14 months ago by
abdul.suboor123 • 0
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... I have aligned the small RNA reads with reference genome, now I want to know the method to count the total number of small RNA both (novel and know) in my reads? any method or tool please mention here, I will be thankful. ...
written 15 months ago by
abdul.suboor123 • 0
• updated
9 months ago by
leukosnanos • 0
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... Same error has showing, even I have Python 3.6 and installed the conda dependencies.
[skabdul@mn02 M1]$ python --version
Python 3.6.5
[skabdul@mn02 M1]$ conda config --add channels defaults
Warning: 'defaults' already in 'channels' list, moving to the top
[skabdul@mn02 M1]$ c ...
written 16 months ago by
abdul.suboor123 • 0
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... Thanks for your quick response, The commands you have mentioned above are still not working with me.
[skabdul@mn02 M1]$ python -m pip install Circle-Map
/bin/python: No module named pip
[skabdul@mn02 M1]$ conda install -c bioconda circle-map
Fetching package metadata .... ...
written 16 months ago by
abdul.suboor123 • 0
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... I have followed your instructions and try to use Circle-Map tool but it is showing error. Please tell me what's wrong with it.
[skabdul@mn02 M1]$ circle_map.py ReadExtractor -i qname_M1_map.bam -o circular_read_candidates.bam
/public/home/skabdul/software/Circle-Map-master/circlemap/cir ...
written 16 months ago by
abdul.suboor123 • 0
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