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This might be a system incompatability, but when I try to ran the code, it gave me an error about bc_gene_umi_subsampled not being a data table. Adding the setDT function fixes it.
> setDT(bc_gene_u…
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We currently censor some tiles and cycles based on poor error rates from the interop files. There is currently no way to upload that interop data to BaseSpace from an old run, it can only be uploaded …
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Hi, thanks for your previous responses a while back.
I am now trying to use cellSNP/Vireo with a SAM/BAM output file from `salmon alevin` instead of Cell Ranger, and wanted to see if this would be …
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Hi,
Is there any chance swappedDrops could be run on STARSolo output?
Currently STARSolo outputs barcodes.tsv, features.tsv and matrix.mtx but no h5 files.
While swappedDrops requires h5 file…
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Hi,
I am encountering the same error as mentioned. I have scDNAseq fastq files. I am running the following pipeline in nonormal mode:
```
chisel_prep \
-r /rsrch5/home/tdccct/ppshah/shared/gen…
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[dump.hex.checklog.txt](https://github.com/littlebalup/PyPS3tools/files/11147091/dump.hex.checklog.txt)
text copy of file is shown below:
```
PyPS3checker v0.11.x. Check log.
Checked file : …
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Hello,
I am running cellSNP in mode 2 for my bam file with the following command:
```
cellSNP -s \
-O \
-b \
-p 10 \
--cellTAG=None \
--UMItag=UB \
--minMAF 0.1 \
--minCOUNT 100 \
--…
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Hi @Xiaojieqiu I have the same problem that @ikwak2 (issue #20) but with the markerDiffTable function. It appears this error: `Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE) : invalid charac…
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On your README page, you mention that READ2 should be specified first and then read1. In the help page of STAR and other places, but also in the README, you give the example of READ1 then READ2: --rea…
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Trying to analyse some SMART-SEQ3 data and can't manage to get past the mapping step. Any suggestions would be much appreciated. I've remade my index multiple times (`STAR --version` is giving 2.7.3a,…