Hi everyone,

I have a question regarding a chip-seq pipeline I am adapting to my analysis.

As first, I sorted and indexed my BAM files, then I used the following script to remove duplicates and multi mappers.At the end, I obtained two folders, one with no duplicates with BAM and BAI files, one with no multi mappers with only BAM files.

I know that I will need BAI files in the next steps. Can I merge the two folders even if my files have different names?

Or can I create the BAI files using samtools or another tool?

Hope my explanation is not too confusing...

thank you in advance for the help

 #!/bin/bash

    bamtools="/home/anaconda3/bin/bamtools"

    io="/media/jay/Data/ChipSeq_data"
    mkdir -p $io/BAM/duplicates/
    mkdir -p $io/BAM/multimappers/

    cat > $io/filter.json <<- EOM
    {
    "isMapped" : "true",
    "mapQuality" : ">4"
    }
    EOM

    for i in `ls -1 $io/BAM/sorted/*.sorted.bam`
    do
      sample_name=`basename $i ".sorted.bam"`
      echo "$i => $sample_name"
      # mark and remove duplicates
      duplicates="$io/BAM/duplicates/$sample_name.removed.dup.bam"
            java -Xmx8G -jar /home/jay/picard/build/libs/picard-2.27.4-SNAPSHOT-all.jar MarkDuplicates \
        INPUT=$i \
        OUTPUT=$duplicates \
            METRICS_FILE=$io/BAM/duplicates/$sample_name.metrics.txt \
            OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 \
            CREATE_INDEX=true \
            REMOVE_DUPLICATES=true
      # remove multimappers after removing the duplicates
      multimappers="$io/BAM/multimappers/$sample_name.filtered.bam"
      $bamtools filter -in $duplicates -out $multimappers -script $io/filter.json
    done