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Hello,
I have 2 10X Genomics datasets (BCR and GEX). What are the appropriate parameters setting for TRUST4?
I'm using
f"run-trust4 -1 {f1} -2 {f2} --barcode {f1} --UMI {f1} --readFormat bc:0:15,…
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Dear Dev,
I am new user of TRUST4 on single cell TCR seq analysis, regardless, TCR seq could be successfully obtained using bulk RNAseq data.
I wonder, with my 3' 10x genomics GEX data (I have b…
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On this page:
https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/technology_visium.html#technology-focus-10x-genomics-visium
The plotting examples don't look like t…
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Thank you for the great method!
Regarding this algorithm, I'd like to ask whether it is suitable for spatial transcriptomic dataset, such as 10x Genomics Spatial Transcriptomics. If applicable, do …
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Hi! I'm brand new to using immunarch and am preparing to use it to analyze some cellranger vdj data from 10x genomics. I was a little confused in the "Loading 10x Genomics Data" vignette, because orig…
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Hi,
For SC5P chemistry, I should be able to define 0,0,16:0,16,26:0,26,0 for the 1st read and 1,0,1:1,0,1:1,0,0 for the 2nd read in -x parameter.
Can this be done?
Best
Pasi
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Dear Peter,
We were hoping that hapCUT2 would allow us to skip LongRanger to phase variants. However, we are running into some issues, and I would like to check back with you regarding some questio…
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Hey guys!
I am running TRUST4 on 10xGenomics RNAseq data. Especially, we make use of the AIRR file for our post-processing analysis.
For a QC protocol, we require the `cell_ids`, however I see tha…
mapo9 updated
3 months ago
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From the vignette and by running the SCnorm command on 10x data that is heavily zero-inflated (sequenced to 85-90% saturation), i ran into the
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Hi ,thanks for developing such a good tool
and if convenient ,I am looking forward to the part for 10x genomics Chromium 3' library,and very curious about when it will be uploaded.
Thanks!