I recently downloaded Tablet to assess read coverage of my de novo assembly of RNA-Seq of marine snail venom duct tissue. I have tried to run a script supplied by Tablet, coveragestats.py, which will give me: number of coverage values (=contig length), average depth, percent of bases with a depth greater than zero (percent coverage), and maximum depth.
I get the following error when I try to run the script
Traceback (most recent call last): File "coveragestats.py", line 91, in stats = '\t'.join(templateStr) % tuple([func(coverages) for func in funcList]) File "coveragestats.py", line 71, in average return float(sum(ints))/float(len(ints)) ZeroDivisionError: float division by zero
I am fairly certain this is happening because when I load my .bam and reference files to Tablet I get the following warning:
The index for this BAM file is reporting a total read count of zero. Although this may be correct, it is more likely that the index file was generated prior to read metrics being available. It is advisable to recreate this index using samtools 0.1.8 or higher.
I have verified my version of samtools as being the latest version and have reindexed my .bam file several times. Still the same problem (read count 0). However I do see the number of reads associated with my contigs in the Tablet header (and they are displayed), just not in the actual list of contigs in the left panel where this info should be associated to each contig.
Thanks in advance for any help.
I get the following error when I try to run the script
Traceback (most recent call last): File "coveragestats.py", line 91, in stats = '\t'.join(templateStr) % tuple([func(coverages) for func in funcList]) File "coveragestats.py", line 71, in average return float(sum(ints))/float(len(ints)) ZeroDivisionError: float division by zero
I am fairly certain this is happening because when I load my .bam and reference files to Tablet I get the following warning:
The index for this BAM file is reporting a total read count of zero. Although this may be correct, it is more likely that the index file was generated prior to read metrics being available. It is advisable to recreate this index using samtools 0.1.8 or higher.
I have verified my version of samtools as being the latest version and have reindexed my .bam file several times. Still the same problem (read count 0). However I do see the number of reads associated with my contigs in the Tablet header (and they are displayed), just not in the actual list of contigs in the left panel where this info should be associated to each contig.
Thanks in advance for any help.
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