over 900 million bases in CCDS regions?
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5 weeks ago
Yiming • 0

Hello,

I have a BAM file (hg19) and need to calculate the depth of coverage at each base in the exonic regions. I downloaded the CCDS BED files from the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=1109848749_gHXtAmBqKaR1UOA191fS812ba8pn&clade=mammal&org=Human&db=hg19&hgta_group=genes&hgta_track=ccdsGene&hgta_table=0&hgta_regionType=genome&position=chrX%3A15%2C578%2C261-15%2C621%2C068&hgta_outputType=bed&hgta_outFileName=ccds.bed) and used samtools depth

However, I found there are over 900 million bases in the CCDS file, which much exceeds the expected bases in exonic area (roughly 1%). I manually checked the bed file with R and got the similar output of 900 million bases (995030607) for non-overlapping regions

I wonder what the problem might be and I could obtain a BED file obtaining all human exonic regions?

Thank you very much!

CCDS • 194 views
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You can find the current CCDS data at this NCBI site. You should be able to create a BED file from information there. Take a look at the README to understand the data.

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To my understanding, the data here, especially the newer ones, are built on GRCm38, while my data uasd hg19 as reference genome

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What did you pick in the second screen - One entry per gene or per coding exon or something else?

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