chromosome length .size file

Hey all,

I am trying to make a .size file that lists the length of each chromosome from a genome file (e.g. fasta file)

Here is an example of the desired output:

chr1    248956422
chr10   133797422
chr11   135086622
chr12   133275309
chr13   114364328
chr14   107043718
chr15   101991189
chr16   90338345
chr17   83257441
chr18   80373285
chr19   58617616

...

I am currently writing a script that uses awk '{ print length }' but I am wondering if there is a tool available so that I don't have to reinvent the wheel?

Thanks in advance

chromosome genome

• 2,444 views • link

updated 3.4 years ago by Ram

• written 6.1 years ago by brismiller •

duplicate:Sequence length from Fasta ; How to count the length of fasta sequences? : ....

• 0 views • link

written 6.1 years ago by Pierre Lindenbaum

Thanks for that Pierre, I just found out that I could cut samtools fai f1 and f2 to get what I want.

• 0 views • link

written 6.1 years ago by brismiller •

0 answers

No answers yet.

More posts like this

Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
written 2.2 years ago by asalimih •

Hello, I'm annotating a deepvariant vcf file using vep ensembl version 110.1. however although the allele depth shows obvious heterozygous variant the `ZYG` output of …
Biostrings readDNAStringSet handling of N bases
written 4.9 years ago by rubic

Hi, I'm using `Biostrings` `readDNAStringSet` to read the human genome fasta file : GRCh38.p13.genome.fa (`search.genome.fn` in the code below). ``` search.genome.set <- Biostrings::readDNAStringSet(search.genome.fn) ``` Then …
How can I get this sorted by ascending order? (when the number and character is together)
written 7.1 years ago by woojoy14 •

samtools view NA12878_dedup.bam | cut -f 3 | sort -u > chr.list8 > chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr2 …
Bedtools coverage confuses chromosomes
written 7.6 years ago by wsciekly.maciek •

I have a problem running bedtools coverage (bedtools v2.26.0 ): my bed file is: 9 137618991 137619028 EHMT1 0 + Y 14056216 14056289 VCY1B 0 …
MAFTOOLS HELP - Mutational Signature
written 8.9 years ago by David_emir

Hi All, I am trying to run mutational signatures on my MAF file, using maftools (https://github.com/PoisonAlien/maftools). while trying to run this i am constantly My …
Error with correctGCBias in deepTools
written 9.5 years ago by clmin •

Hello, I'm trying to correct the GC bias with deepTools. I successfully used computeGCBias > computeGCBias -b file.bam --effectiveGenomeSize 2150570000 -g mm9.2bit -l 200 --GCbiasFrequenciesFile …
variant analysis and filtering from annotation file
written 9.7 years ago by garimav89 •

I have a annotation.txt file like this : chr1 34567 A chr2 12345 C chr14 14567 T chr15 32456 A I want to extract data …
[GATK] Weird error using Picard SortVcf on COSMIC file
written 10.5 years ago by umn_bist •

I tried sorting my COSMIC vcf using Picard's SortVcf function to match my reference dictionary order. This was after an error using MuTect2 and visiting …
problem with methylKit of the annotation
written 11.6 years ago by hua.peng1314

I am dealing with RRBS data follow [the manual][1]. I met some problem when doing annotation.The problem showed below. ``` > read.transcript.features("mm9.refseq.genes.bed",remove.unsual=TRUE,up.flank=1500,down.flank=500,unique.prom=TRUE) > diffAnn <- …
Error Import File With "Import" Of Rtracklayer
written 14.5 years ago by ska007 •

<p>Hi, This is related to a the question found here (http://biostar.stackexchange.com/questions/3414?sort=newest#sort-top). I am trying to import a gff file using import("file.gff") which contains a set …