User: mustafa_aljadi
mustafa_aljadi • 10
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Posts by mustafa_aljadi
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... Hi All,
I have many fastq.gz files that I want to extract them from one directory to another one. Can you please tell me which linux command I should use?
Thank you
...
written 5 weeks ago by
mustafa_aljadi • 10
• updated
5 weeks ago by
GenoMax ♦ 96k
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A: Pac bio assembler
... I am trying to make an assembly by PAC bio reads of beaver. it's already done by canu but the results weren't good enough. so I am looking for other assemblers that can do the assembly. Also, I am thinking to trim these but I don't know what is a good trimming program for PAC bio reads. Any sugges ...
written 6 weeks ago by
mustafa_aljadi • 10
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Hi All,
I have a PacBio raw data I want to assemble, what is the list of good assembler to assembler available?
Thanks
...
written 6 weeks ago by
mustafa_aljadi • 10
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... Dear All
I used CLC workbench to BLAST after I got my results I wanted to extract the result as CSV or Excel file. But unfortunately every time I extract the BLAST result from CLC workbench the file is empty. Also, this happened when I tried to extract the mapping result as a bam format. Can yo ...
written 9 months ago by
mustafa_aljadi • 10
• updated
9 months ago by
GenoMax ♦ 96k
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A: fastq-dump -I --split-files
... Sorry I didn't get this part of your answer Just define number of threads available and the output directory. Put this script in your sra file directory and change permission with chmod u+x script. Can you please verify it to me?
Thanks
Mustafa ...
written 14 months ago by
mustafa_aljadi • 10
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A: fastq-dump -I --split-files
... I already download the files from NCBI. To transfer the 75 RNA seq files to CLC program those files need to be split into reverse and forward.
I did use this code fastq-dump -I --split-files SRR390728.sra, which is applicable for example for one SRR390728. My question is how can I split the 75 R ...
written 14 months ago by
mustafa_aljadi • 10
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Hey All,
I am trying to do RNA seq on CLC, but before transfer my data to the program I need to split the reads that I have into forwarding and reverse. There is a program called fastq-dump -I --split-files that does this process. The problem which I have is the 75 RNA seq files has it's own SRR ...
written 14 months ago by
mustafa_aljadi • 10
• updated
14 months ago by
ATpoint ♦ 46k
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A: Assembly of wheat genome
...
Thank you so much. I really appreciate your help guys.
Mustafa ...
written 2.6 years ago by
mustafa_aljadi • 10
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Comment:
A: Assembly of wheat genome
...
Thank you so much guys for your help.
Mustafa ...
written 2.6 years ago by
mustafa_aljadi • 10
12
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779
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9 follow
4
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Hey All,
I am working on the DNA assembly of the wheat genome. I used the W2rap assembler, the assembly is done. But I dont know how to determine if my assembly is good or Not?
I mean which criteria I should follow?
Thanks in advance
Mustafa
...
written 2.6 years ago by
mustafa_aljadi • 10
• updated
2.6 years ago by
shengweima • 60
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