Measuring sequence length in "bp"

Question

[dpidad]

Given a sequence as below:

@SRR211279.25468524 HWUSI-EAS404_106009863:7:120:17892:21339 length=200
CCAACCTCTACCCATNACCCAGTTCCGAAGTTGCTTCCACATTTTCAGGTATCTTTATAGNNATGCTCCAGTCCTCATTTGCCATTTTTGGTAANANTTANCTNTGTANTCTCCGNNNTNNNCNCTNGCNATNTNANANNNTTCANTNNNNNNNNNNNNNNNANNNNNANTNANANATTTCNGAGCCCCCCCAGANGCAG
+SRR211279.25468524 HWUSI-EAS404_106009863:7:120:17892:21339 length=200
IIIGIIIIIIGGGGG%DEEEEDBDEIHIIIHIIIIIIIHIDHIHHIIIGGIGIIIGEEEE%%;==><;>>IIIIHIIIIIIIIIIIIIIIGDDD%8%;;8%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

What is the length of the sequence? 200 bases? or 200base pair(bp) or 100bp? What tool is recommended for measuring the length in "bp" for FASTA/FASTQ File?

Answer 1

[Devon Ryan]

Technically, base pairs refers to double-stranded sequences. Practically speaking, however, "base pair" and "bases" are equivalent, so the length is 200 regardless. BTW, wc -c will count the number of characters in a line for you (you'll need to subtract 1 from the result).

[PoGibas]

Devon, you can use echo -n(no need to subtract 1) :-)

echo -n ACGT | wc -c
4

dpidad, try fastqc for measuring lengths of your reads in fastq. More solutions here: Sequence Length Distribution From A Fastq File

[Devon Ryan]

Just goes to show, regardless of how long I've been using the CLI, there's always something useful to learn! :o)

[dpidad]

Thanks for the clarification.

I got this read file from ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR211/SRR211279/SRR211279.sra. When extracted (using fastq-dump) got the SRR211279.fastq file with each reads of length 200bp. However, came across a paper referring "SRR211279 (25.23M 100bp paired-­end reads generated by Illumina GAIIx) from the Washington University Genome.
From where to get the SRR211279 100bp paired end read files?

I'm using this files with Soap3-dp, which needs 2 read files for pair-end rund. Venturing new into these topics, any pointers would be helpful.

[Devon Ryan]

You forgot the --split-files or --split-spots option. fastq-dump is not the best designed program in the world, since it really should do this automatically.