Bo Sun

> Hi, > When you run sctransform normalization you are standardizing the expression of each gene in each cell relative to all the other cells in the input matrix. That...

Hi, sure thing, this was for chemistry v3, but I have tried it for V1 and V2, same thing happens. Each time I adjusted the ranges to fit the chemistries...

Sorry, our cluster locks out copy and pasting the output and I have to keep the study IDs of the samples confidential. But yes it occurs just as the fastq-extractor...

Hi, yes I took it from a local installation of cellranger and uploaded it on our cluster within a custom directory that I then supply the absolute path to. The...

it is just the absolute paths to the locations: for our system its `/groupdir/users/username/projects/projectx/gex/XXX_1.fastq.gz /groupdir/users/username/projects/projectx/gex/XXX_2.fastq.gz /groupdir/users/username/reference/cellranger_whitelists/v3/3M-february-2018.txt` I would be surprised if that is an issue as trust4 runs to completion...

Oh right. sorry. R1 `@XXXXX.1 1 length=28 CNAAGCGAGCTTACGACGCCTTTCATGC +XXXXX.1 1 length=28 F#F,FF,FFFFFFF:,FFFFFFFFFFFF @XXXXX.2 2 length=28 AATGCCAAGAACGCGTAGACATCTAGCT +XXXXX.2 2 length=28 FFFFFFFFFFFFFFFFFFFFFFFFFFFF @XXXXX.3 3 length=28 CCTCACACACAACCGCTTCTGGTGCAGA` R2 `@XXXXX.1 1 length=151 GAAGAATGGTACAAATCCAAGTTTGCTGACCTCTCTGAGGCTGCCAACCGGAACAATGACGCCCTGCGCCAGGCAAAGCAGGAGTCCACTGAGTACCGGAGACAGGTGCAGTACCTCACCTGTGAAGTGGATGCCCTTAAAGGAACCAAAA +XXXXX.1...

Sorry, can I just add a request onto the same issue chain. Is it possible to index the annot.fa with the report.tsv or cdr3.out? or Add read counts into the...

Thanks for the update on the whitelist issue and ongoing troubleshooting. For the indexing, what I have noticed, is that there are multiple duplicated assemble ids. e.g. assemble0 occurs up...

Thanks, that makes sense. However, I remain a little confused how trust4 works in this case: - Is the consensus assembly then the most abundant assembled contig from a group...

That would be great. Thank you. Alternatively, if the fully assembled contig could be added to the report.tsv and cdr3.out file, that could be good as a user can then...