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JiekaiLab / scTE

MIT License
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RNA-seq data processing #94

Open l1y1y opened 4 months ago

l1y1y commented 4 months ago

Thank you very much for your help, thank you

I want to know if this tool can handle RNA-seq data, or can it only handle single-cell data?

I wish you good luck with your research

jphe commented 4 months ago

Yes, you can run scTE with bulk RNA-seq data, but need to set with the option-CB False -UMI False --hdf5 False

l1y1y commented 4 months ago

Yes, you can run scTE with bulk RNA-seq data, but need to set with the option-CB False -UMI False --hdf5 False

Thank you, thank you for your answer

l1y1y commented 4 months ago

Yes, you can run scTE with bulk RNA-seq data, but need to set with the option-CB False -UMI False --hdf5 False

@jphe hello， I ran the program, used RNA-seq data, added annotation files, and set CB False -UMI False --hdf5 False, but my results seemed weird. Can you help me check the results? Is it correct? Thanks barcodes,(CATTC)n,0610005C13Rik,0610006L08Rik,0610009B22Rik,0610009E02Rik,0610009L18Rik,0610010F05Rik,0610010K14Rik,0610012D04Rik,0610012G03Rik,0610025J13Rik, AC125544.1,AC126027.1,AC126029.1,AC126029.2,AC126031.1,AC126031.2,AC126031.3,AC126031.4,AC126040.1,AC126040.2,AC126041.1,AC126046.1,AC126254.1, ,Adgre1,Adgre4,Adgre5,Adgrf1,Adgrf2,Adgrf3,Adgrf4,Adgrf5,Adgrg1,Adgrg2,Adgrg3,Adgrg4,Adgrg5,Adgrg6,Adgrg7,Adgrl1,Adgrl2,Adgrl3,Adgrl4,Adgrv1,Adh1,Adh4,Adh5,Adh6-ps1,Adh6a,Adh6b,Adh7 Gm11472,Gm11473,Gm11474,Gm11475,Gm11476,Gm11478,Gm11479,Gm11480,Gm11481,Gm11482,Gm11483,Gm11484,Gm11485,Gm11486, Olfr844,Olfr845,Olfr846,Olfr847,Olfr848-ps1,Olfr849,Olfr850,Olfr851,Olfr852-ps1,Olfr853,Olfr854,Olfr855,Olfr856-ps1,Olfr857,Olfr858-ps1,Olfr859,Olfr860,Olfr861-ps1,Olfr862,Olfr863-ps1, ,0,1,74,1040,21,54,1,20,157,36,5,15,6,0,1110,63,2,1422,73,38,0,679,68,208,3,1,33,13,2,2,21,0,0,24,349,587,14,26,235,312,17,2,0,5,4,0,6,12,31,270,75,36,690,16,713,162,990,5,0,10,19,174,251,0,12,0,2 A csv document was generated with only these contents. After I read it, there were two rows and more than 50,000 columns. I would like to ask, should I process this result? I added an annotation file. Shouldn’t the output result be the name of the gene?

jphe commented 4 months ago

It's correct, the column name is gene name

l1y1y commented 4 months ago

It's correct, the column name is gene name

OK, thank you and wish you good luck in your research