Entering edit mode
4.4 years ago
ksipes
•
0
I am wanting to be able to view the percentage of reads from metagenomic bins to the paired fastq files. I have already completed making .bam files, and .sam files and sorted, and indexed the sam files with samtools.
I just need the percent of reads from my bins that are found in any of the seven paired end reads that I have. Assume that I have all of the correct files and am just looking to view the output.
Thanks for your help in advance.
How do I figure out the percent of reads that went into each of the bins that mapped to ? In the beginning, I concatenated my .fa files for my index file to mapp against all of my paired fastq files. Now i just want to know the number of reads from the fastq files make up each one of the bins.
You have the number of reads mapped to each sequence, you can sum them up for each bin.
That previous command shows the reference sequence name (NODE_###_##...) and then all of the contig mapped numbers. How does adding up the reads mapped to each sequece show me the percent of reads from each bin when I don't know what contigs from each fastq went into which bin ?
Sorry, I lost you .