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I am following these commands. However, I am getting blank output file.
minimap2/minimap2 -x ava-pb -t8 pb-reads.fq pb-reads.fq | gzip -1 > reads.paf.gz
# Layout
miniasm/miniasm -f reads.fq reads…
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Hello,
I'm using epic 0.2.9 to compare two mapping samples against a mapping reference, and I have some questions for you.
I'm looking for enriched regions of unknown size comparing two experimental…
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Hi,
I am using STAR 2.7.3a for extracting unmapped reads with the --outReadsUnmapped Fastx. I found that the number of unmapped reads in both mate1/2 is different from the Log.final.out output.
T…
ghost updated
3 years ago
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In the new_mbg/bonobo folder, there are 36 t2t scaffolds in the original MBG version vs 24 w/new. The files t2t_scaffolds_by_chr list the t2t scaffolds and their chromosome IDs. These both used trio-s…
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Using BWA MEM to map WGS reads to metagenomic contigs, it is possible to find no reads mapping to a small number of short contigs. This then results in inferring contig coverages of zero and an inabil…
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Hello,
I'm trying out DAMAPPER for mapping a set of unitigs to PacBio reads, and when parsing the results I notice that sometimes duplicate alignments to different parts of the same read are reporte…
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Hello,
I am working on RNA-seq data, that consists of 150 bp paired-end reads and I was hoping to align them to the already published reference genome of the some species. Genome size is: ~3300000…
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We assembled a set of 11 genomes of the same crop species with hifiasm version 0.19.8-r603. One of the 11, lineA, was an outlier in terms of overall assembly size. Particularly, 8Mb of the 5’-end of …
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Dear developers,
This tools looks super interesting! I wonder if you have tried it coupled with Read Until functionality for cDNA or other "short" long reads (e.g. 1-2kbp).
If not, do you think …
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Hi, Dr. Song
I successfully generated alignment.maf using AnchorWave and converted it into a BAM file using the provided script. However, when I attempted to convert the BAM file to a VCF file using …