Our new service,
All of the hints here are for using a Linux-type operating system. If you are using a mac some of these commands will work in the terminal. If you are using windows, you should probably see if you can get access to a Linux machine!
First, you need to download the data. We recommend cURL for that! Copy the
curl -Lo results.zip http://22.214.171.124/results/0e1c6dd49b2/results.zip
After uncompressing the zip file you will most likely have many directories, each of which contains some results. We combine those into a single directory. Note that the number of directories depends on the number of SRA runs you search against. The most is about 45 directories, but you may have many fewer. Adjust the number here as appropriate.
for i in $(seq 1 45); do mv $i/* bamfiles/; rmdir $i; done
This creates a single directory with all the results. At the moment, we don’t remove
find . -size -421c | xargs rm -f
Because this also deletes some of the index files, we delete all those and remake them. We could be more precise about this, but this step takes a couple of seconds so we don’t care!
rm -f *.bai
for bamfile in *.bam; do samtools index $bamfile; done
Note, if that rm -f command fails, you can try this one:
find . -name \*bai | xargs rm -f