sumeetg23

If you want the I7 indexes on a standalone FastQ file (R2 file will have the I7 indexes), then 

    Step 1. first modify your RunInfo.xml file by changing  

        <Read Number="2" NumCycles="8" IsIndexedRead="Y" />  

        to  

        <Read Number="2" NumCycles="8" IsIndexedRead="N" />. 

sumeetg23

Step 1.3, Step 2.1 to 2.3 and Step 3.1 can be done for a given fastq file and reference fasta using the following shell script: https://github.com/sumeetg23/Tools/blob/master/Shell/CRISPR-Generate-Count.sh

Step 3.2 script is available here: https://github.com/sumeetg23/Tools/blob/master/R/CRISPR_CountSummary_v1.2.R

Step 1: Generate Bowtie Index

Step 1.1 (if file not in fasta format)

  Input - Tab delimited text file with column 1 as a unique ID and column 2 as the sequence.