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User: abdul.suboor123

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Posts by abdul.suboor123

<prev • 40 results • page 1 of 4 • next >
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Comment: C: Extracting matrix columns specific to file1 and file 2, not the overlap or commo
... Thanks for your reply, yeah actually, i was extracting specific rows @Bastien Herve , it works for me. ...
written 6 weeks ago by abdul.suboor123 • 0
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Extracting matrix columns specific to file1 and file 2, not the overlap or common?
... 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 ...
matrix sequence columns written 6 weeks ago by abdul.suboor123 • 0 • updated 6 weeks ago by Bastien Hervé ♦ 4.5k
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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 9 weeks ago by abdul.suboor123 • 0
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How to get the reads with significant RPM?
... 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 ...
rpm small rna rna-seq written 9 weeks ago by abdul.suboor123 • 0
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How to count total small RNAs (known and novel) in my aligned reads?
... 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. ...
small rna counts srna written 12 weeks ago by abdul.suboor123 • 0 • updated 12 weeks ago by shawn.w.foley • 1.1k
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Comment: C: Problem in setting pipeline for circDNA prediction analysis.
... 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 4 months ago by abdul.suboor123 • 0
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Comment: C: Problem in setting pipeline for circDNA prediction analysis.
... 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 4 months ago by abdul.suboor123 • 0
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Comment: C: Problem in setting pipeline for circDNA prediction analysis.
... 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 4 months ago by abdul.suboor123 • 0
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Comment: C: Circle-Map: Sensitive detection of circular DNA at single-nucleotide resolution
... Please let me know, why it is still not working with me? below is the pipeline and the error shows when I entered the pipeline. [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 4 months ago by abdul.suboor123 • 0
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Answer: A: How to perform sequence validation of NGS data?
... @Bastien Hervé , I have a little knowledge of Python, but I am not good at python. Yes I have SnapGene sequences and sanger sequeced files. Please tell me the trick how I can do that? Yeah for each sequence I need a junction in sanger sequence. ...
written 10 months ago by abdul.suboor123 • 0

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Voter 5 weeks ago, voted more than 100 times.
Popular Question 5 weeks ago, created a question with more than 1,000 views. For While using ggtree in rstudio, it shows error in some commands
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