Hi. I feel like this might be a stupid question, but I can't seem to find an answer anywhere. I'm currently trying to align my paired-end reads to a reference genome. To do this, I believe I need to create a ".sam" file using "bwa".
However, what I don't understand is, should I create one .sam file that contains all of my paired-end samples? That is, I have around 100 samples that are paried-end (so, in total, 200 files). Should I align all of these samples to the reference genome "in one go" so that I have one large .sam file containg all my 100 samples? Or should I create 100x .sam files where I've aligned each sample separately?
My goal later is to find SNPs of these samples.
Thanks!
1 answer
If each "sample" is an independent specimen then one usually produces one alignment per sample. Don't use sam files, use bam right away. SAM is human-readable, by this uncompressed, therefore large and takes up space. DOwnstream things like variant calling run on the binary bam format.
bwa mem (options...) | samtools view -o out.bam
Log in to answer this question.
-
Where can I get gtf file for Adenovirus 5?
written by new •
-
How to find DNA sequence of a SNP without reference genome? (I have a .vcf file)
written by Roland •
-
PCR-duplicates and RAD-sequencing
written by Roland •
-
Any tutorial how to "link" SNPs with genes?
written by Roland •
-
STACKS pipeline. Confused about paired-end with "ustacks".
written by Roland •
-
Hisat2
written by Pegasus •
-
Comparing fastq files
written by diffexp123 •
-
What does the reference_id = -1 indicate in a .sam file read with pysam?
written by osman.christof •
-
Variant Calling - for multiple samples need advice
written by David_emir
-
Merging all left / all right reads before STAR align?
written by Biogeek
You can use
read groupsto include multiple samples in one alignment file (see: https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups ). If you are planning to use GATK for SNP calling then this may indeed be a requirement.