User: Mostafa Mahmoud

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Posts by Mostafa Mahmoud

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Perl script review
... i run it but it gives wrong mapping ################################################################# Running assemply on sample repA2 ################################################################# CMD: spades.py --rna -k 25 -t 6 -1 reads2.left.fq.gz reads2.right.fq -2 -m ...
written 3 months ago by Mostafa Mahmoud0
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Comment: C: Perl script review
... it just maps the parameters and read the sample and run every in sample file line one by one cat sample file cond_A cond_A_rep1 A_rep1_left.fq A_rep1_right.fq cond_A cond_A_rep2 A_rep2_left.fq A_rep2_right.fq cond_B cond_B_rep1 B_rep1_left.fq B_rep1_ ...
written 3 months ago by Mostafa Mahmoud0
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Comment: A: Perl script review
... actually, I am new to Perl I wrote this script to run spades by reading the samples one by one from a text file but when I run it shows nothing and I can't figure out where is the problem ??? ...
written 3 months ago by Mostafa Mahmoud0
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Perl script review
... I wrote Perl script to run spades commands but the script doesn't process the cmd #!/usr/bin/env perl use strict; use warnings; use Getopt::Long qw(:config no_ignore_case bundling); use FindBin; use Cwd; ###################################################### ## ...
perl spades written 3 months ago by Mostafa Mahmoud0 • updated 3 months ago by Michael Dondrup45k
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Comment: C: Trinity assembly resources
... I Tryed one sample is ok. ...
written 3 months ago by Mostafa Mahmoud0
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Comment: C: Trinity assembly resources
... i just export my PATH apps and simply add the command in file then qsub denovo.sh cat denovo.sh ---------------------------------------------------------------------------------------------------------------------------------------- export PATH=/bin:/sbin:/public/home/jmwu/.linuxbrew/bin:/public/ho ...
written 3 months ago by Mostafa Mahmoud0
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Trinity assembly resources
... hi, I have 60 samples 10g of RNA seq I using Trinity to do denovo assembly but i can't figure out resource usage i am running using qsub to submit it main node every time job canceled i don't know why the server have 2tb memory. ...
assembly rna-seq written 4 months ago by Mostafa Mahmoud0
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Comment: C: Make a .gmt file using bash for loop
... this command is great but in long line give truncate output damage the format. ...
written 7 months ago by Mostafa Mahmoud0
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Comment: A: convert Trinotate resulte to GFF file
... second question is how to convert Trinotate.xls to gff do you have any idea. ...
written 8 months ago by Mostafa Mahmoud0
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Comment: A: convert Trinotate resulte to GFF file
... Thats it fin great jop thank you very much. ...
written 8 months ago by Mostafa Mahmoud0

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