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                                            tdfyoder

ImmunoSeq TCRB v4B V2 Export: Input Parsing Error

Thank you for the prompt response; I will send you a subset. If I come across any other errors do you want me to post here or a new thread?

Questions about the analysis of BCR/TCR using the bulk RNAseq

@mourisl could you please point me in the direction of some literature regarding #2 above? Specifically, BCR lamba/kappa expression > heavy chain? Thank you.

Questions about the analysis of BCR/TCR using the bulk RNAseq

thank you @mourisl !

problem with downloading databases

experiencing same problem here, failed under 'standard' build. ``` Step 1/2: Performing rsync file transfer of requested files rsync: link_stat "/all/GCF/030/643/825/GCF_030643825.1_ASM3064382v1/GCF_030643825.1_ASM3064382v1_genomic.fna.gz" (in genomes) failed: No such file or directory (2)...

problem with downloading databases

I've downloaded and unzipped the 16/8 std dbs found below. Temporary solution. https://benlangmead.github.io/aws-indexes/k2

problem with downloading databases

Perhaps NCBI has updated their repository (?), I was able to proceed w/o rsync errors today- bacteria genomes. ``` kraken2-build --download-library bacteria ```

Error in hclust(d, method = method) : size cannot be NA no

Hey zznx, I had the same error. I subset my seurat object to less than 65536 cells and it worked fine. -Todd

Input for createContrast()

Hey @JudithBernett , I have a similar question. How did you resolve this issue? -Todd

BiocParallel errors

hello, I have rec'd a similar error. I can confirm the same ref fa was used for alignment and bam files are in order. I downloaded primary assembly hg fa...