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{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Using gc_extrap on mitochondrial target enrichment data","articleBody":"Hello!\r\nIm working with gc_extrap with data has been enriched for mitochondrial genome (MT) and Im unsure what is the best way to proceed, or if is even adequate to use preseq with enriched data. I have bam files that have been generated by mapping to the full genome (i.e. nuclear + mitochondrial). So firstly, what Im doing:\r\n\r\n1) Creata mr file from bam file: to-mr -o ${WHATEVER}.mr ${WHATEVER}.bam\r\n2) Sort mr file: sort -k 1,1 -k 2,2n -k 3,3n  ${WHATEVER}.mr  -o ${WHATEVER}_sorted.mr \r\n3) Intersect the sorted mr file with MT, to get mr file with reads only from MT: bedtools intersect -a ${WHATEVER}_sorted.mr  -b MT.bed \u003e ${WHATEVER}_MT.mr \r\n4) Run preseq gc_extrap on the intersected mr file: preseq gc_extrap -v ${WHATEVER}_MT.mr  -o ${WHATEVER}_gc_extrap.txt\r\n\r\nSecondly, if I can do this or if there is any other way possible to run gc_extrap with enriched data, can I transform the output to be mean coverage across the mitochondria and number of raw sequenced reads, instead of total number of unique base pairs and total number of sequenced base pairs. I was trying to divide the number of unique base pairs by the size of the mitochondrial genome and the total number of sequenced base pairs by the reads length. However, for one sample its coverage is suppose to saturate at ~2 coverage. However, I have ~110 coverage, empirically calculated with GATK...\r\n\r\nAm I doing something wrong, or am I unable to gc_extrap on my data?","author":{"url":"https://github.com/eugeniosss","@type":"Person","name":"eugeniosss"},"datePublished":"2024-04-18T09:21:20.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":3},"url":"https://github.com/73/preseq/issues/73"}