User: MSM55

gravatar for MSM55
MSM5590
Reputation:
90
Status:
Trusted
Location:
Israel
Last seen:
1 week, 3 days ago
Joined:
1 year, 11 months ago
Email:
s***********@gmail.com

Posts by MSM55

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Blast many sequences
... I am not able to understand what you are trying to do because your question is not explain properly but I can explain you the steps you can do. **Convert .fastq to .fasta** sed -n '1~4s/^@/>/p;2~4p' file.fq > file.fa **Use BLAST Command Line Application for fasta file** [manual][1] ...
written 8 months ago by MSM5590 • updated 8 months ago by biokoala3.6k
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Comment: C: Decision on no. and type of libraries to be generated for plant genome assembly
... You are right long read are important in assembly, to handle repeat region and to get good quality of assembly. How this calculation is done of number libraries and amount of data to be produced ? Can you please explain this calculation despite of budget ...
written 8 months ago by MSM5590
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Comment: C: awk command to count specific field
... Hi, You can use following command awk '$7==1 && $8==1 {print}' input.txt ...
written 8 months ago by MSM5590
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Comment: C: awk command to count specific field
... I am not able to Understand input file format. You can use following command to count number of 1 in field 2 grep -o ",1" input.txt | wc -l ...
written 8 months ago by MSM5590
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Decision on no. and type of libraries to be generated for plant genome assembly
... I want to sequence a plant genome whose estimated genome size is of 600 Mb. My question is how to decide: - number and type of libraries (paired end and mate pair) on different platforms (PacBio, Illumina) - amount data required - read length - insert size (mate pair) - coverage An example of the ...
genome assembly library pacbio illumina written 9 months ago by MSM5590
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Comment: C: epitope analysis for multiple sequenes
... You can use LWP or WWW::Mechanize module in perl. ...
written 9 months ago by MSM5590
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Comment: C: epitope analysis for multiple sequenes
... Can you send me the IEDB software command so I can write script for you. Are you using Linux or any other operating system ? ...
written 9 months ago by MSM5590
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Comment: C: epitope analysis for multiple sequenes
... You can write a bash script and just loop (for/while) over each sequence ...
written 9 months ago by MSM5590
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Comment: C: Force script to finish even if it fails.
... You can try following code. total_files=`find -name '*.fastq' | wc -l` arr=( $(ls *.fastq) ) for ((i=0; i<$total_files; i+=2)) { sample_name=`echo ${arr[$i]} | awk -F "_" '{print $1}'` echo " $sample_name" MyPipeline.sh ${arr[$i]} ${arr[$i+1]} } ...
written 10 months ago by MSM5590
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Comment: C: using parallel program
... reformat the post according to below post ...
written 11 months ago by MSM5590

Latest awards to MSM55

Teacher 11 days ago, created an answer with at least 3 up-votes. For A: bwa for multiple fastq files

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