User: MSM55
MSM55 • 120
- 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
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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
MSM55 • 120
• updated
12 months ago by
Vijay Lakhujani ♦ 4.2k
0
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1
answer
370
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1
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... 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
MSM55 • 120
0
votes
3
answers
528
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3
answers
... Hi, You can use following command
awk '$7==1 && $8==1 {print}' input.txt ...
written 13 months ago by
MSM55 • 120
0
votes
3
answers
528
views
3
answers
... 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
MSM55 • 120
2
votes
1
answer
370
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7 follow
1
answer
... 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 ...
written 13 months ago by
MSM55 • 120
0
votes
1
answer
256
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1
answers
... You can use LWP or WWW::Mechanize module in perl. ...
written 13 months ago by
MSM55 • 120
0
votes
1
answer
256
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1
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... 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
MSM55 • 120
0
votes
1
answer
256
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1
answers
... You can write a bash script and just loop (for/while) over each sequence ...
written 13 months ago by
MSM55 • 120
0
votes
2
answers
426
views
2
answers
... 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
MSM55 • 120
0
votes
3
answers
570
views
3
answers
Comment:
C: using parallel program
... reformat the post according to below post ...
written 15 months ago by
MSM55 • 120
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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