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Recent Replies
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Look inside the `*.log` files to see if you can get additional clues (and post them here, if you can't figure out things). Check for lines …
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You can run Scrublet before filtering cells with high gene counts and compare the doublet score vs `n_counts_genes`.
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In first instance you will as you say need to assign GOterms to your genes. eggNOG-mapper is certainly a valid approach to do this indeed. …
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@colindaven thanks a lot! `clinker` also seems to be a nice/effective tool to do so. It happens we stuble across a work where they used `Ci…
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Why not use something like Jbrowse2 instead ? https://jbrowse.org/jb2/gallery/
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This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
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[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
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@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
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Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
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Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
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The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
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Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
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Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
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