I am experimenting with BowTie vs BWA. Now, I have to do experiments for various length reads. So, I am trying to find 180, 200, 240 bp read length databases. Can anybody help me where and how I can get those databases. I have tried to find here. However, unable to find. Can anybody help me on this ? Thanks in advance.
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Arpssss •
You may also want to experiment by generating reads with a read simulator from different genomes. It is a quite eye opening experience to see perfect reads not matching back to the genome.
Bowtie2 comes with a nice read simulator. Istvan is right. Understanding multiple hits and mapping oddities is a great exercise.
The short read archive will have what you want.
That's a really long read for Illumina. I don't know if anyone has sequenced reads that long, or if the Illumina machines are capable of that. I'm assuming you are interested in Illumina, and you want a 240bp read on each end?
If you follow my suggestion below, the longest you'll find from 1000 Genomes are 31 200-bp runs, 1156 202-bp runs, and 32 216-bp runs.
There are a lot of 454 runs that have longer reads though, but people typically don't use bwa or bowtie for that.
It is sometimes hard to find exactly what you want in the SRA. The suggestion to simulate is probably best, but it depends on what you want to do.
If you want to have more data than you can handle, check out the entire set of 1000 Genomes sequencing runs here (~39k sequencing runs total).
You'll have a row for each run like this (edited to come closer to fitting on the screen):
FASTQ_FILE CENTER_NAME SAMPLE_NAME POPULATION EXPERIMENT_ID INSTRUMENT_PLATFORM INSTRUMENT_MODEL LIBRARY_LAYOUT WITHDRAWN READ_COUNT BASE_COUNT
data/NA19238/sequence_read/ERR000018.filt.fastq.gz BGI NA19238 YRI ERX000014 ILLUMINA Illumina Genome Analyzer SINGLE 0 9280498 334097928
data/NA19238/sequence_read/ERR000019.filt.fastq.gz BGI NA19238 YRI ERX000014 ILLUMINA Illumina Genome Analyzer SINGLE 0 9571982 344591352
data/NA19240/sequence_read/ERR000020.filt.fastq.gz BGI NA19240 YRI ERX000016 ILLUMINA Illumina Genome Analyzer II PAIRED 0 149044 5365584
You can look at the READ_COUNT and BASE_COUNT columns to calculate the read length, maybe like this:
$ cat 20120522.sequence.index | cut -f 1,24,25 | awk '{print $1"\t"$3/$2}'
data/NA19238/sequence_read/ERR000018.filt.fastq.gz 36
data/NA19238/sequence_read/ERR000019.filt.fastq.gz 36
data/NA19240/sequence_read/ERR000020.filt.fastq.gz 36
data/NA19240/sequence_read/ERR000020_1.filt.fastq.gz 36
...
You can look through the results to find runs that meet your specifications, or runs that could meet them if you trimmed the reads.
Actually, I have not understand the above procedure properly. What I have to do ? Download ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/sequence_indices/20120522.sequence.index this page and run above command ? But gives error: cat 20120522.sequence.index.txt | cut -f 1,24,25 | awk '{print $1"\t"$3/$2}' awk: (FILENAME=- FNR=1) fatal: division by zero attempted
Hi Arpssss,
"matted" is right that you can't find Illumina reads that are greater than 200 bp in length. 454 sequencer produces reads that could be 500 bp but you dont use bowtie or BWA to align those reads (though both tools are now capable of aligning reads up to 1000 base pairs). I did what "matted" tried to explain you right above my answer. Here is the link to the tab delimited file https://dl.dropbox.com/u/6854830/1000genome_Arpssss.txt . I have added a column called read length in the very end. The spreadsheet has all the runs that have avg. length ranging from 150 to max for the 1000 genome project.
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