1 answer
I assume that "deep" means "depth" here.
Assuming that you have gzipped fastq files, then a simple zcat foo.fq.gz | wc -l will let you know. Just divide the resulting number by 4 and that will tell you if they met the minimum read number they guaranteed. Note that "depth", as typically defined, has no real meaning in RNAseq and should almost* never be used.
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Devon Ryan
There are 4 lines per read.
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Devon Ryan
Because in fastq file, every fourth line denotes your reads, e.g. 2,6,10,14,18,22,26 and so on these lines in fastq is reads sequences, other lines are of different purpose;
- 1st line starts with '@' is your sequence ID for your read
- 2nd line is your read sequence
- 3rd line starts with '+' is something something
- 4th line is quality value of your read which is in 2nd line
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Manvendra Singh
ha aha ha! I was not sure that what to write there, because I never understood the importance of third line :)
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Manvendra Singh
The purpose of the + line was to indicate that the sequence lines were finished (the sequence can be multiline, even if that will break most tools since it's almost never done). These days, however, the + line is just an extra useless 2 bytes.
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Devon Ryan
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