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Hello
I use velocyto to count spliced / unspliced counts on dropseq data
I use the command
`velocyto run -o ./loom/ -m /cluster/huanglab/hhuang/Database/RNA_velocity/rmsk/hg19/hg19_rmsk.gtf /clu…
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Hello,
I'm trying to reproduce the .loom file for the [10X embryonic E18 Mouse Brain](https://www.10xgenomics.com/resources/datasets/fresh-embryonic-e-18-mouse-brain-5-k-1-standard-2-0-0) using veloc…
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Hi Alex,
I have a BAM file from an RNA library, and there is a variant that I can see clearly in IGV. However, for some reason, the Strelka variant caller cannot call it. I noticed that the Cigar …
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The current setup does not use the full power of the local (VM) resources. In particular, GeneSeqer is always run in non-parallel mode, even on a VM with multiple processors.
Performance gains shoul…
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In your paper and documentation you kindly show your command lines. When using STAR, you use the option --outSAMstrandField with IntronMotif which according to STAR manual: "The spliced
alignments th…
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Hi Brian,
I followed the steps, but failed at the final step:
`~/miniconda3/opt/transdecoder/util/cdna_alignment_orf_to_genome_orf.pl transcripts.fasta.transdecoder.gff3 transcripts.gff3 transcript…
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Trying to align two paired reads to a reference genome for which I have created an index. Error I receive is as follows:
Usage: STAR [options]... --genomeDir /path/to/genome/index/ --readFilesI…
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Hi! Thank you for developing such a useful tool! I am running BRAKER using singularity, however the pipeline was interrupted when filtering train.gb for "good" mRNAs. The error at that point was the f…
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Is it possible to add one function to check cigar length == sequence length before samtools calmd, or sometimes it report error
It seems come from this situation: _N_N\*
so it will divide into 3 par…
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With the "pre-mRNA" GTF, there are no splice junctions, which could cause *alignment* issues in CellRanger's snRNA-seq workflow, as discussed here:
https://github.com/10XGenomics/cellranger/issues/7…