beginner984

Thank you for answering me I was trying in windows suddenly I saw you are mentioning that your software not working in windows so I changed to Linux but at...

Thank you very much As I had mentioned I have had `two PBMCs` on them we profiled with `conventional Bulk RNA-seq` and `10X 5' scRNA-seq (GEX)` This time, I run...

Thanks a lot I have used fastq files as input for TRUST4 so I have not filtered anything Im affraid🙁 Sorry I got confused here, as I googled, eveness is...

Thank you very much At the moment I have fastq/bam files from 10x 5' single cell RNA-seq (GEX) I really do not know how to filter those null cells before...

Thank you very much But the question is, which input I should feed into TRUST4 to construct clonotype structure after filtering? I can not understand the relashionship between Seurat and...

Sorry I need your kindly point of view in making some conclusion from my data I have had two healthy `PBMCs`; before running my main experiments on more samples I...

Thank you very much Regarding the Seurat filtering For 5' GEX ``` > list.files() [1] "barcodes.tsv.gz" "features.tsv.gz" "matrix.mtx.gz" > # Load the PBMC dataset pbmc.data

Sorry you meant I should use `trust_barcode_report.tsv` for scRepertoire or Platypus as an input? Shall I use `trust-barcoderep-to-10X.pl` to convert `trust_barcode_report.tsv` first? Although I tried and I got error please...

Thank you, specifying the output file prefix, and it outputs as "XXX_t.csv" did not give error `fi1d18@Server2:/data//TRUST4-master/scripts/TCR/scripts/scripts$ perl trust-barcoderep-to-10X.pl /dataTRUST4-master/scripts/TCR/scripts/TCR/TRUST_PN0340_0002_TCR_S4_L001_R2_001_barcode_report.tsv /data/TRUST4-master/scripts/TCR/scripts/TCR/TRUST_PN0340_0002_TCR_S4_L001_R2_001_barcode_t.csv` But I am confused why from `TRUST_PN0340_0002_TCR_S4_L001_R2_001_barcode_report.tsv` input which...

Thank you very much, although Immunarch was working very smooth with TRUST4_report.tsv file but likely does not work with barcode file even after conversion with the perl script (or might...