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 …
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: $ …
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):
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.
rna seq - Download multiple fastq files using fastq-dump ...
Jul 22, 2020 · Download multiple fastq files using fastq-dump Ask Question Asked 5 years, 5 months ago Modified 5 years, 5 months ago
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 …
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 …
fastq - Remove low quality reads - Bioinformatics Stack Exchange
Jan 24, 2023 · I want to remove reads from FASTQ file that contain homopolymers > 10bp and remove reads with <35 average quality score across the entire read. To remove …
fastq - Running cellranger on scRNASeq data with feature …
Mar 27, 2023 · How did you create your fastq files? If you've run cellranger mkfastq with the correct sample sheet, you should have got separate fastq files for each library: RNA-seq, VDJ …
Fast way to count number of reads and number of bases in a fastq …
Jun 29, 2017 · I am looking for a tool, preferably written in C or C++, that can quickly and efficiently count the number of reads and the number of bases in a compressed fastq file. I am …