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  • Bamutils count question

    hi,

    I am a newbie in using command-line tools for NGS. Just tried to use the bamutils from NGSUtils in processing the bam file from the core. I tried to calculate the RPKM and reads by using the following command:

    ./bamutils count gtf hg19_genes.gtf Tophat.bam

    It runs for a few minutes and returns the following message:
    Reading GTF file...
    GTF file missing isoform annotation! Each transcript will be treated separately.
    Done! (0:28)
    1.6% - 0:12 [> ] ETA: 11:33 | FUCA1Traceback (most recent call last):
    File "/root/ngsutils/bam_utils/bam_count.py", line 222, in <module>
    modelobj.count(bamfile, stranded, coverage, uniq_only, rpkm, norm, multiple, whitelist, blacklist)
    File "/root/ngsutils/bam_utils/count/count.py", line 52, in count
    count, reads = _fetch_reads(bam, chrom, strand if stranded else None, starts, ends, multiple, False, whitelist, blacklist, uniq_only)
    TypeError: 'int' object is not iterable

    So how can I fix it? THX!

  • #2
    Sorry for the late reply...

    Try to update your code that you are using (git pull, if you used git). This bug ended up catching me too, and I wrote the thing... it should be fixed in the repository.

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