Question: Fetching the sequence from the genome
0
gravatar for zunera
4 weeks ago by
zunera0
zunera0 wrote:

Hello everyone,

I have a genome with 4.3 GB size. I have run local blast for it. Now I want to fetch the sequence from the genome like from 700000 bps to 800000 bps. I don't have any information regarding chromosome coordinates or chromosome number etc. because it is a non-redundant data. I have tried to make bed file but it is also not working. I am a beginner. Please help me.

Thank you in advance.

genome • 100 views
ADD COMMENTlink written 4 weeks ago by zunera0
3

Hello and welcome to biostars zunera ,

I have tried to make bed file but it is also not working.

Please show us more details about what you have tried and what is "not working".

Two common ways to receive a region of interest are bedtools getfasta:

$ bedtools getfasta -fi genome.fa -bed myregions.bed

and samtools faidx:

$ samtools faidx genome.fa <chr>:<from>-<to>
ADD REPLYlink written 4 weeks ago by finswimmer11k

Thank you for you reply.

I was using the wrong command for bedtools. The above command worked for me.

Secondly, the bed file was not in tab delimated format. So I used awk command to convert it into tab delimated format and the issue is resolved.

awk '{ for(i=1;i<=NF;i++){if(i==NF){printf("%s\n",$NF);}else {printf("%s\t",$i)}}}' bedfile.bed > output
ADD REPLYlink modified 4 weeks ago by finswimmer11k • written 4 weeks ago by zunera0
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