Tweet
have mapped illumina PE reads to the reference genome using BWA and now, would like to get a consensus sequence of the mapped reads- can samtools be used on the aligned bam file??
-
-
See this thread: http://seqanswers.com/forums/showthread.php?t=14565 (and the other thread mentioned in #4 there). -
samtools mpileup -uf /<reference.fasta> <aligned.bam> | bcftools view -bcg - > <intermediate.bcf>
gave me an error: -bash: syntax error near unexpected token "<
I was wondering BCFtools are part of samtools, right?- is this the correct comand?Comment
-
You don't literally use < > around the file names.Comment
-
has anyone tried this command to generate a consensus file
samtools mpileup -uf reference.fasta sorted_alignment.bam | bcftools view -cg - | vcfutils.pl vcf2fq
but where should I put the output file name???Comment
-
Originally posted by mmmm View PostCode:$ samtools mpileup -uf reference.fasta sorted_alignment.bam | bcftools view -cg - | vcfutils.pl vcf2fq > output_file_name
Comment
-
yes- thanks.
I will ignore the abnormal shapes that appeared after the sequence
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Comment
-
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...Yesterday, 07:01 AM -
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM
Comment