An overview of Illumina multiplexing

Multiplexing Index 1 (i7) is always read. Index 2 (i5) is read only in dual index setting. Single indexing Dual indexing Single end (SE) R1, R2 R1, R2, R3 Paired end (PE) R1, R2, R4 R1, R2, R3, R4 Multiplexing - dual index reads - paired end

June 10, 2018 · 1 min · Firas Sadiyah

Preparing genome reference in FASTA format

To prepare genome reference in FASTA format for mouse assembly NCBI37/mm9, we have two options: From UCSC Using the mm9 assembly from UCSC golden Path. Do not use the masked file chromFaMasked.tar.gz! 1# download `chromFa.tar.gz ` from UCSC golden path 2wget 3#or 4sync -avzP rsync:// . 5 6# uncompress the downloaded file 7tar -xvzf chromFa.tar.gz 8 9# remove `*random.fa` chromosomes 10rm -rf *_random.fa 11 12# concatenate all FASTA files into a single file 13cat *....

December 10, 2017 · 2 min · Firas Sadiyah