More posts like this
-
What is the correct procedure to generate a consensus bacterial sequence?
written by marongiu.luigiHello, I would like to create a consensus sequence of a bacterium starting from the fastq files generated with Illumina. I proceeded as follows: 1. …
-
The accession number of generated consensus sequence and reference sequence
written by mngpn •I was using samtools, bcftools, vcfutil.pl and seqtk to generate consensus sequences from some raw SARS-CoV-2 fastq data, but I do not know why the …
-
CD-HIT: representative sequence vs consensus sequence
written by rDNA •Hi, with the CD-HIT command `cd-hit-est` it is possible to form sequence clusters. Per cluster, 1 "representative" sequence is generated, as stated at the CD-HIT …
-
samtools idxstats showing accession number and genomic scaffold
written by whb •Hi, Is this an expected output for `Samtools idxstats`? Why is it showing accession instead of chromosome number? most of the NC_... corresponds to a …
-
Is it possible to download Genebank files from NCBI having organisms names as the file name?
written by K.Gee •Hello, BIOstars! I am looking to download a specific bunch of full genomes from NCBI https://www.ncbi.nlm.nih.gov/assembly/ I typed my desired organism and then from the …
-
Reconstruct reference sequence from SAM file?
written by eholleman •I am aligning a consensus sequence to a reference genome using Bowtie2 and I am interested in the nucleotide sequence of the reference where the …
-
Refseq accession number for protein and nucleotides
written by horsedog •Hi, I have a basic question about the accession number in reference sequence. For non-redundant protein is WP_ and for nucleotides is NZ_. Here I …
-
how to include insertion and deletion in the consensus sequence from BWA reference mapping/assembly
written by liaoyunshi •Many thanks for reading my post. When I finish NGS, I use BWA to conduct reference mapping/assembly to align short reads into the reference genome, …
-
Generating consensus sequences
written by Lina FHi all, I am interested in generating consensus sequences from a bwa alignment. I generated the consensus sequences as follows: samtools mpileup -uf reference.fasta sorted.bam …
-
pysam fetch with partial reference name
written by yarmda •I'm new to pysam and trying to parse a bamfile by a RefSeq Accession number. However, that accession number is only part of the reference …
A title of a consensus sequence depends on a program that you use to calculate the consensus. An accession number is a reasonable variant for a title.
How to deal with the situation if the name of consensus sequence generated from a sample is changed to the same as reference sequence after consensus generation?
FASTA files are just text files, you can change their headers any way you like. Don't you know how to edit text files?