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Results tagged with fastq
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user 6251
FASTQ is a file format use to store short reads and their quality values
1
vote
How to measure the total size of a fastq file in base pairs?
Using Perl:
Print the sequence lines (line number 2, 6, 10, etc). Remove the newlines with chomp. Count the bytes (here, bases) using wc -c:
perl -ne 'if ( $. % 4 == 2 ) { chomp; print; }' | wc -c
- 841
5
votes
Accepted
Telling grep to treat N as [ATCG]
If you want to stick to grep, use a scripting language such as Perl to generate the regex programmatically. For example:
perl -le 'print join "", map "[${_}N]", split //, $ARGV[0];' ATCGCTATCG
Print …
- 841
3
votes
Error with BWA Mem input having multiple fastq files using cat and process substitution
"<(cat A.read2.fq B.read2.fq ...)"
1
Oddly enough, process substitution inside double quotes works at least in the case I tested before posting: bwa mem -M test1.fa "<(cat test_assembler_tiny_1.1.fastq … )" "<(cat test_assembler_tiny_1.2.fastq)" This contradicts the answer here: https://unix.stackexchange.com/q/486019 . …
- 841