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At one locus in this dataset I see that iVar is soft-clipping all the bases except 1 when that base is next to an insertion and mismatches the reference.
I've also included illumina data from the sam…
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Hello,
I have a project that requires alignment of WGS Illumina data on specific regions of the hg38 reference genome. I want to speed up the whole process, so I do not have to map my reads to the …
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```##### ERROR MESSAGE: SAM/BAM file /gpfs/project/projects/spike/Intermediate/085_gatk_PrintReads/Keimbahn/KB0006_c.reCal.reAl.nodup.srt.bam is malformed: Error parsing SAM header. DT tag value '2016…
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We downloaded the pre-compiled index file and tried to run with the files in the example folder. It did not produce expected results, an empty output file. We also tried with our own data, Illumina an…
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Hi, I am trying to assemble a plasmid using paired-end Illumina reads from a whole genome sequence with Oxford Nanopore long reads from a plasmid DNA extraction from the same organism.
The command …
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https://github.com/theodorc/Atlas-CNV/blob/673a8e741c06e15a8612ba295bf7ff56e8c38774/convert_GATK_DoC.R#L39
Dear authors,
Could you tell the reason that you choose 100 as the average read…
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AlphaFold's team just published a new tool - AlphaMissense:
https://www.science.org/doi/10.1126/science.adg7492
Calculated predictions are available at https://zenodo.org/record/8208688 (link take…
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When processing SRA RNA-seq fastq files with Fastool as part of the Trinity package, Fastool appends a /H to the end of sequence ids which then causes errors downstream in Trinity.
Here are the first…
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Hi
Any plans to expand snippy with support for pacbio and nanopore reads? Noticed this tutorial demonstrating the cool stuff snippy can do https://training.galaxyproject.org/training-material/topic…
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Project: ENCODE
So - we are working with a new High Throughput Sequencing Assay: icSHAPE, that captures RNA secondary structure.
NTR: "icSHAPE"
Editor preferred term: "icSHAPE"
Alternative…