What is the difference between FASTA, FASTQ, and SAM file formats?
FASTA and FASTQ formats are both file formats that contain sequencing reads while SAM files are these reads aligned to a reference sequence. In other words, FASTA and FASTQ are the "raw data" …
Good / recommended way to archive fastq and bam files?
Apr 11, 2023 · It can do lossless compression of gzip-compressed fastq files, bam files, and even cram files, and achieves really good size reduction (image from the PetaGene webpage):
linux - How to get a file with the number of reads for several fastq.gz ...
Feb 4, 2023 · 4 I have generated several FASTQ files and I would like to know the amount of reads for each of them. I am planning to run FastQC on the files which I know would give me the number of …
How to split FASTQ reads without re-running `fastq-dump`?
May 9, 2020 · I forgot to add the --split-3 option to my fastq-dump command. Is there an easy and fast way, without re-downloading the files, to split the reads in half and write them to two output FASTQs?
python - How do you write a .gz fastq file with Biopython ...
Jun 24, 2017 · The record is a SeqRecord object, fastq is the file handle, and "fastq" is the requested file format. The file format may be fastq, fasta, etc., but I do not see an option for .gz.
How to measure the total size of a fastq file in base pairs?
Sep 1, 2020 · Using a fastq parser in Python (for instance the one provided by mappy), it is rather straightforward to compute the sum of the lengths of the sequences present in a fastq file: $ python3 …
quality control - Bash scripting FastQC for multiple fastq files in ...
Oct 26, 2018 · I am completely new to bioinformatics so I'm looking to learn how to do this. I have multiple directories with fastq files: E.g; 10 Directories with each time series, each with Treatment …
rna seq - How do I determine read length from a user-inputted fastq ...
Dec 10, 2022 · Can you guide me on how could take an input fastq file, read the length from read and then feed it into the findtail's command? I have suggested concerns about documentation and …
rna seq - Download multiple fastq files using fastq-dump ...
Jul 22, 2020 · Download multiple fastq files using fastq-dump Ask Question Asked 5 years, 4 months ago Modified 5 years, 4 months ago
bash - How to merge .fastq.qz files into a single .fastq.gz with their ...
I have a large number of .fastq.gz files of different lane and reads. I have to merge them each reads group files into single .fastq.gz files. **eg: 1st type NA24694_GCCAAT_L001_R1_001.fastq.gz