Mike Stubbington

Hi Omar, Please check to see if you have done the following: 1. Download the separate internal_data directory from ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data and put it into the same directory as the IgBlast...

Hi Omar, You should have a path as follows: `/home/repository_software/ncbi-igblast-1.7.0/bin/internal_data` where the `internal_data` directory came from: ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data. Do you have that? If not, please download that directory from the NIH...

Hi @oeco28, Were you able to resolve this? I'll close this issue if it's now working for you. If not, let me know, and I'll be happy to help. Best,...

Hi Derek, Sure, please have a go at this. Thanks! How easy would it be to make something that would work across both BraCeR and TraCeR (www.github.com/teichlab/tracer )? That’d be...

Hi Linda, Have you increased the memory available to your docker image? Have a look at the last paragraph in the docker section of the readme: https://github.com/teichlab/bracer#docker-image Let us know...

Can you try giving it more memory? Your data is likely bigger than the test set. > On 10 Aug 2018, at 23:20, Linda-Lan wrote: > > Hi Mike, >...

Hi Stijn, Are you using all built-in sequence references? It looks like the TRAV29_DV5*03 allele isn’t in https://github.com/Teichlab/tracer/blob/master/resources/Hsap/raw_seqs/TCR_A_V.fa so Tracer can’t extract the sequence to make a full-length version based...

Yes, I think that alignment rate looks about right. If you’re managing to assemble TCR sequences then it’s sufficient :) Cheers, Mike > On 13 May 2019, at 18:55, micans...

You should be fine to use a transcriptome reference downloaded from BioMart as detailed here: http://www.nxn.se/valent/2016/10/3/the-first-steps-in-rna-seq-expression-analysis-single-cell-and-other Best, Mike > On 13 Feb 2020, at 11:53, Tommaso Andreani wrote: > >...

Ah yes. "Transcript Stable ID" is equivalent. Very best, Mike > On 13 Feb 2020, at 13:11, Tommaso Andreani wrote: > > Hi Mike, > > thank you for your...