What is the difference between FASTA, FASTQ, and SAM file …
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 …
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 …
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 …
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 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 …
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: $ …
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
rna seq - How do I determine read length from a user-inputted …
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 …
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 …
bash - How to extract all pair end fastq.gz files from multiple ...
Jul 1, 2019 · I have all file names for each paired-end fastq pair as shown below. Could you please suggest how I can extract all fastq.gz files in a single folder? sample name: …