Pall Melsted
Pall Melsted
Which workflow are you using to go from the BUS file to a gene count matrix compatible with seurat? Somewhere in the translation the names might be messed up or...
Can you grep your cdna fasta file for `ENST00000425848`. This is a transcript for one of the alternative genes for HLA-B. If it's in the index then kallisto will pseudoalign...
While GTF and GFF3 are mostly the same there is a difference in how the free format field of attributes is formatted and used. kallisto currently only supports GTF files,...
Is this the run you were using? SRR7868083 Which transcriptome did you use for building the index?
This is the results I get when I use the Ensembl transciptome reference version 93. ``` kallisto quant -i ~/work/data/human/Homo_sapiens.GRCh38.93.cdna.all.kidx -o out SRR7868083_1.fastq.gz SRR7868083_2.fastq.gz -t 4 [quant] fragment length distribution...
This is most likely an inconsistency in the reference genome and the gtf, namely having to do with chromosome names. Can you show the bam header and the first few...
There is an inherent 32bp limit on barcodes, this captures most technologies out there since the barcode can be defined as only the variable parts, i.e. spaced by fixed sequences....
The quick work around is to "stare" at the 96 variable 16bp sites and pick 10bp parts from each that are at a long hamming distance from each other. Anything...
Don't know if this was fixed in v0.29