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I have problems creating the refflat from the gtf file. It has been reported more often, I followed all suggestion, and as far as I can see the gtfs's look OK. I have one where it works:
```
1 gram…
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Hej,
I just got some data, generated with SureCell libraries on a ddSeq machine (i.e. the protocol by Illumina and Bio-Rad). I would like to test your pipeline for the analysis but I'm not sure if …
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Rather major stuff! as discovered by @Marlies1993
`bwa mem` yields empty alignments for sequences of 25bp ...
apparently it isn't designed for 25bp, and something like `bwa aln` should be used inste…
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Hello,
I get the following error after following the manual for a single-cell dataset I'm working with.
data_obj = featureConstruct(normalized,method = "SelfProjection")
Error in cor(fpkm_for_clu…
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Hi, Alex
Apologies if I have missed this somewhere, and I am trying to process my 10X data with STARsolo. This is very convenient. But if there were more than one barcode and UMI molecular in my s…
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Hi folks,
I'm trying dropSeeqPipe for the first time on some test Nadia data we generated. I am using the example Nadia template config and I have 4 samples, each with paired-end 125bp reads.
…
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Hi, I am using popscle demuxlet using this command:
singularity exec ../code/popscle_2021-05-05-da70fc7.sif popscle demuxlet \
--plp subset_pileup/subset_samples_to_demuxlet.pileup \
--vcf line…
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Hi,
Thanks for developing this very useful and much needed tool!
I am running step4 option A and it seems like it cannot identify any valid SAMrecords in my file.
The command I am running is …
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_Our analysis re- veals that the BTD-trained SenCID is applicable to both Dropseq- (Figures 2A, 2C, 2D, and 2F) and Smart-seq- (Figure 2B) generated single-cell data._
Is there any difference betwe…