Hello,
I am attempting to use samtools faidx to pull down a sequence to do some visualization in R. My current code reads:
(within R)
system(sprintf("samtools faidx Genome/hg38.fa chr:36287064-36287162,intern = TRUE)[[2]])
But unfortunately, the R only outputs the first 60 nucleotides. When I run the samtools faidx function on command line, I can see that the second line is below the first 60nt.
Is there a samtools option I can specify to have it be on a single line? I can write an R script to figure that out, but I would like to avoid that, as this range/size will change and not all ranges will be over multiple lines.
Thank you!
•
written
by
ryan.leenay •
1 answer
There is no built-in option in samtools faidx to output an one-line fasta. However you can pipe the output into awk to get the desired format, as explained in this thread.
Log in to answer this question.
-
variant calling through gatk
written by ashaneev07 •
-
Errors when using samtools faidx and bgzip for indexing human reference genome
written by hello_bioinf •
-
About hg38 reference genome indexing
written by kwanghoon •
-
Samtools consensus for WES files
written by sidjain •
-
SAM doubt about sampileup
written by psschlogl •
-
Similarity between reference files
written by Gene_MMP8
-
Error in Adding 1000Genomes Ancestral Allele info: Using VCF tools fill-aa
written by shrutishreyajha •
-
samtools faidx redirection
written by biomagician
-
How to align 100 samples with BWA?
written by madkitty
-
Extracting subsequence from FASTA using Samtools faidx not working
written by hmg •
