User: MSM55
MSM55 • 70
- Reputation:
- 70
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- Location:
- Israel
- Last seen:
- 1 week ago
- Joined:
- 1 year, 7 months ago
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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 3 months ago by
MSM55 • 70
• updated
3 months ago by
Vijay Lakhujani ♦ 3.0k
0
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210
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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 4 months ago by
MSM55 • 70
0
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3
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297
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3
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... Hi, You can use following command
awk '$7==1 && $8==1 {print}' input.txt ...
written 4 months ago by
MSM55 • 70
0
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3
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297
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3
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... 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 4 months ago by
MSM55 • 70
2
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1
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210
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7 follow
1
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... 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 4 months ago by
MSM55 • 70
0
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1
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137
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1
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... You can use LWP or WWW::Mechanize module in perl. ...
written 4 months ago by
MSM55 • 70
0
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1
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137
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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 4 months ago by
MSM55 • 70
0
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1
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137
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1
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... You can write a bash script and just loop (for/while) over each sequence ...
written 4 months ago by
MSM55 • 70
0
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2
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247
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... 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 5 months ago by
MSM55 • 70
0
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3
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327
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3
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Comment:
C: using parallel program
... reformat the post according to below post ...
written 6 months ago by
MSM55 • 70
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