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):
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 …
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?
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 …
ncbi - How can I download multiple SRR* files at a time when using ...
Mar 7, 2024 · How can I download multiple SRR* files at a time when using sratoolkit's fastq-dump? Ask Question Asked 1 year, 10 months ago Modified 1 year, 4 months ago
What is the index fastq file (sample_I*.fastq.gz) generated when ...
What is the index fastq file that comes with some Illumina sequencing datasets? (The samplename_I*.fastq.gz file.) For example, I recently received some 10X Chromium reads for two …
FASTQ file trimming - Bioinformatics Stack Exchange
Jun 8, 2020 · What application are you using that will be okay with a mismatching quality string? Use trimmomatic or cutadapt, or bcl2fastq could probably do the job too. Those will also have the benefit …
Compressing read data (converting fastq to fastq.gz) on Windows
Jun 27, 2022 · I downloaded some of my data in fastq format instead of fastq.gz. I want to upload my data on a server now. I was wondering if there is a way to convert my fastq files to fastq.gz on …