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We appear to have an unsolved problem with assemblies that have multiple Covs.
From @rchikhi in an earlier issue: "Among the 10,816 datasets of the master table, 272 (2.4%) of them have CoV contigs…
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While aligning a 19nt-long sequence to the human reference genome (hg38) using `bwa aln`, I get the unexpected results to get less reported alignments when using 6 mismatches instead of 5.
My toy e…
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```
In PairedReadsMapping.cpp:14,48 and ReadsMapping.cpp:15,44, change
"\nInfo %d: %d CPUs %s.\n" -->
"\nInfo %d: %d CPUs detected. %s.\n"
In ParameterList.cpp:180 change
"Each read has a maximun %…
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- Two main data generation strategies: (1) amplicon sequencing and (2) shotgun sequencing
- At this time analysis one can choose calling variants or performing within-host evolution analyses inclu…
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My problem is that I am having difficulty obtaining a list of variants using bcftools mpileup and bcftools call with PacBio data. I do not have this problem with data of Illumina paired-end sequencing…
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Hi,
thanks for this interesting tool. I am current trying to get ularcirc to run with some of my data.
Unfortunately, the reference genome for alignments don't match the UCSC chromosome naming…
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Hello, I used cactus to align 10 primate whole genomes (fasta files of ref genomes downloaded from UCSC, soft repeat-masked). Job took around 12-13 days, confirming the expected runtime. (used `cactus…
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Hi,
I generated bam files by aligning to the genome and outputting the alignments in transcriptome coordinates by setting --quantMode TranscriptomeSAM in STAR. Then I tried to randomize the bam fil…
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Hi Alex,
I have RNA-Seq data from hybrid mouse (C57BL and 6NJ). The reference mouse genome is from C57BL. This is my first time to deal with hybrid, I have seen some options in STAR that talk abou…
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Hello,
I am trying to run vg deconstruct on a vg file that I created from whole genome alignments. However, the command did not generate any output. None of the subcommands worked for deconstruct (…