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  • Tophat reads that weren't used for mapping?

    Hey,
    I was running TopHat for the first time for paired-end reads which were 101 bp long. Since it was a test run, I only performed it for the first 500,000 reads that were in each fastq file. I noticed that before it aligns/maps the left and right ends to the hg19 build, it got rid of 19 reads from the left file and 7 reads from the right file.

    In case you are wondering about the output below, 'reads_in' is 487,355 and not 500,000 in each file because the original fastq files were quality filtered using the fastxtoolkit. This would remove reads independently in each file and so I had to use a script to find intersecting/matching pairs from the first 500,000 reads in both the filtered fastq files. That resulted in 487,355 with the remainder being orphaned (I will map this later separately)

    cat left_kept_reads.info
    min_read_len=101
    max_read_len=101
    reads_in =487355
    reads_out=487336

    cat right_kept_reads.info
    min_read_len=101
    max_read_len=101
    reads_in =487355
    reads_out=487348


    Does anyone know why this happens when TopHat is run? Also, is there a way I can find those left out reads, maybe using the output bam file and the 2 original fastq files?

    Also, what is traditionally the next step after obtaining this bam file? This is a part of an RNA-seq analysis.

    Any help would be greatly appreciated.



    Thanks
    Last edited by vkartha; 04-18-2012, 07:54 AM.

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