totally agree ! +1
Can anybody indicate me how to search efficiently for human whole genome sequence data (fasta/q files)- with a certain read length and coverage?
I am aware of the 1000 genomes project, but I have not found yet a tabular listing of the used read length....further more I find the samples description rather confusing.
Thanks
steffi
2 answers
I would say the tasks you are looking for is not possible at this moment. The read lenghts are not information that is usually thought to be important/essential to warrant a special searchable field.
Also I think that the concept of fixed read length is just a limitation/characteristic of a sequencing technology rather than being permanent attribute that characterizes all data.
Since the ftp site in the 1000 genomes is accessible remotely via wget, you could query the second line of each file and count the number of characters like this:
wget -qO- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/sequence.index | awk '{print $1}' | \
grep -v FASTQ_FILE | head | while read fe; do echo $file; wget \
-qO- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/$file | gunzip -c | head -n 2 | \
tail -n 1 | wc -c; done
data/NA19238/sequence_read/ERR000018.filt.fastq.gz
37
data/NA19238/sequence_read/ERR000019.filt.fastq.gz
37
data/NA19240/sequence_read/ERR000020.filt.fastq.gz
37
data/NA19240/sequence_read/ERR000020_1.filt.fastq.gz
37
data/NA19240/sequence_read/ERR000020_2.filt.fastq.gz
37
data/NA19238/sequence_read/ERR000021.filt.fastq.gz
37
data/NA19238/sequence_read/ERR000022.filt.fastq.gz
37
data/NA19238/sequence_read/ERR000023.filt.fastq.gz
41
data/NA19238/sequence_read/ERR000024.filt.fastq.gz
37
[...]
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