gencore
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OpenGene
Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
Hello, I am running the latest gencore with --no_duplex and -s = 3. However, I am still getting many reads output which have the same UMI and identical mapping coordinates....
after deduplication, they are paired read according to the flag value, but there are one or three reads with the same name. Why does this happen?
Hello, After deduplicating with gencore I am getting a number of errors with GATK's ValidateSamFile: - ERROR::MISMATCH_MATE_ALIGNMENT_START, Mate alignment does not match alignment start of mate - ERROR::MISMATCH_FLAG_MATE_NEG_STRAND, Mate negative...
hello, I meet some mistake with the gencore (Version: 0.17.2): 1 contigs in the bam file: chr1: 7249 bp Mismatched UMI of a pair of reads Left: 0:0, M:0:0 TLEN:0...
Error message as: "ERROR: Wrong base with value 0", then no output and hanging.
I am glad to see this tool for generating consensus reads. Unfortunately it does not work with some types of data. For example, where library prep chemistry allows for multiple...
I tried to generated the QC report with coverage statistic in bed scale, When I used a smaller bed, such as the example one, I can get the nice plot....
i use gencore in my pipeline, and i would like to know if its possible to manage versions like your fastp tool in the opengene.org website ? a version control...
I use the gencore to deal with bam file which has the umi info ,but the output file in some position inconsensus with the description. the reads pair1 has the...
Hello, I'm trying to use gencore as described with the simple examples in the README, and some of the resulting files get the error ``` [W::bam_hdr_read] EOF marker is absent....