User: MSM55

gravatar for MSM55
MSM55120
Reputation:
120
Status:
Trusted
Location:
Israel
Last seen:
3 months, 1 week ago
Joined:
2 years, 4 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 12 months ago by MSM55120 • updated 12 months ago by Vijay Lakhujani4.2k
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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 13 months ago by MSM55120
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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 13 months ago by MSM55120
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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 13 months ago by MSM55120
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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 13 months ago by MSM55120
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Comment: C: epitope analysis for multiple sequenes
... You can use LWP or WWW::Mechanize module in perl. ...
written 13 months ago by MSM55120
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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 13 months ago by MSM55120
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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 13 months ago by MSM55120
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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 14 months ago by MSM55120
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Comment: C: using parallel program
... reformat the post according to below post ...
written 15 months ago by MSM55120

Latest awards to MSM55

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: bwa for multiple fastq files

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