JiekaiLab scTE issues - Githubissues

JiekaiLab / scTE

MIT License

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The number of cells is not consistent with the result of cellranger

#96 Yuanqingq opened 2 weeks ago
1
"IndexError: list index out of range" when using scTE_build

#95 BitterWood closed 3 weeks ago
5
RNA-seq data processing

#94 l1y1y opened 1 month ago
5
scTEATAC error

#93 cyyisbest opened 1 month ago
0
Questions regarding preprocessing and integration of scTE with other tools

#92 zerostwo opened 1 month ago
1
How touse output from scTE pipeline to generate a Seurat object

#91 OwenHoare1989 opened 1 month ago
0
Why do I encounter this error when opening scTE?

#90 l1y1y opened 1 month ago
6
Requires python >= 3.9, not 3.6

#89 dannyconrad opened 2 months ago
12
filterCRs IndexError:list index out of range

#88 bio-xtt opened 2 months ago
7
gene expression from scTE were not consistent with cellranger

#87 baishengjun opened 2 months ago
2
Master

#86 carmarpe closed 2 months ago
0
ValueError: Invalid Mode: uR

#85 Kiliankleemann opened 2 months ago
3
How do I find which ones are TEs and which are genes?

#84 gdolsten opened 2 months ago
1
Output matrix with a series of numbers in gene/TE names

#83 synnimeng closed 1 month ago
4
Broad cell type clustering from TE counts alone

#82 sabrinacamp2 closed 3 months ago
1
Wrong example of ATAC

#81 dantingz opened 4 months ago
1
Warning message Query V350183366L1C005R01400986149/1 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.

#80 yc508 opened 4 months ago
2
IndexError: list index out of range

#79 Kiliankleemann opened 6 months ago
4
How scTE infers TEs from scRNA-seq

#78 swainasish closed 4 months ago
0
scTE exon/UTR TE counts inclusion

#77 bosscrab1 opened 7 months ago
1
running for a while but not sure what the progress is

#76 umaarora opened 7 months ago
1
For the same bam file, why is there a big difference in the total number of umi tools quantities and scTE quantities?

#75 SMU-TK-2022 closed 8 months ago
0
running scTE on Parse-seq data

#74 mellyS opened 8 months ago
0
depracation waring and filenotfounderror

#73 Kiliankleemann opened 9 months ago
0
Can scTE handle plate-based single cell sequencing data, like Smart-seq

#72 Guangsheng357 opened 10 months ago
0
Only detecting 3 cells expressing at least 200 genes

#71 t1nnenissen opened 10 months ago
2
no hdf5 out and file not found error

#70 liuyuchenlab opened 11 months ago
6
Details about running scTEATAC in 10X format

#69 zys-BIG closed 10 months ago
3
Too few genes when applying scTE on scATAC-seq data

#68 Wei-BioMath closed 10 months ago
1
Wired Gene name in output h5ad file

#67 XiaoyuZhan520 opened 11 months ago
1
'Calculating expression' getting killed

#66 noranekonobokkusu opened 11 months ago
1
scTE cannot run due to a lack of "="

#65 rpisalive opened 11 months ago
2
Difference between two version of hg38.exclusive.idx

#64 XiaoyuZhan520 opened 12 months ago
1
The input file unassigned_alignments.bam has no cell barcodes information

#63 tinnenissen opened 1 year ago
2
Coordinates of TE duplicates (dup1 ... dupn)

#62 cdelacalle opened 1 year ago
0
scTEATAC

#61 zhaomengmengxiaokeai opened 1 year ago
1
scTE returns empty csv files

#60 CHoeltermann opened 1 year ago
4
Suggestion - more inclusive tags for barcodes

#59 CHoeltermann opened 1 year ago
1
error kindly help

#58 amitpande74 opened 1 year ago
2
how to understand the output file ?

#57 lxlovelxc closed 1 year ago
0
scTE: TypeError: no supported conversion for types: (dtype('<U4'),)

#56 chaigsh opened 1 year ago
11
"outSAMmultNmax" STAR argument for multimapping reads?

#55 rargelaguet opened 1 year ago
1
Remove "U" mode from open()

#54 olivertam closed 1 year ago
2
How to make hg38.exclusive.idx

#53 TheBorgy opened 1 year ago
1
TE file and species issue

#52 zuodabin opened 1 year ago
2
Not getting significant read counts

#51 A1aNNN opened 1 year ago
3
Hidden Dependency on SAMtools and Question Regarding STARsolo Runs

#50 ColeWunderlich opened 1 year ago
2
Unable to recognize barcode information

#49 A1aNNN closed 1 year ago
0
Detect 0 cells expressed at least 200 genes, results output to out.csv

#48 ruocensong opened 1 year ago
3
imposible to read output file

#47 JavieraVillar opened 1 year ago
2