sdparekh zUMIs issues - Githubissues

sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

GNU General Public License v3.0

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issues

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zUMIs didn't create gene_names.txt in the output folder

#396 JinsyWang closed 1 month ago
1
Calculating TPM or FPKM

#395 gevro opened 1 month ago
0
BUG

#394 nhu-github opened 2 months ago
1
R error during counting step before demultiplexing.

#393 dfmoralesb opened 2 months ago
0
Error in using zumis to analyse transposon

#392 ROund-code opened 3 months ago
0
error in using zUMIs to processing smartseq3 data

#391 GGboy-Zzz opened 4 months ago
0
Cannot get the example data from Google Drive

#390 RoseMary93 opened 4 months ago
1
Question：How zUMIs detect Barcodes and why the sum of second column in BCstat.txt is not equal to the sum of input reads number？

#389 bioinfotec opened 5 months ago
0
Error with Corrrecting UB tags when working with large sample size

#388 kvn95ss opened 5 months ago
0
aligning to multiple genomes?

#387 brennaremick closed 5 months ago
1
The .git/objects/pack file is so huge

#386 bioinfotec opened 5 months ago
1
[main_cat] ERROR: input is not BAM or CRAM

#385 Thomas0194 closed 5 months ago
2
Beginning zUMIs from unmapped, tagged, corrected BAM out of fqfilter_v2.pl

#384 biobenkj closed 6 months ago
7
Issues while starting zUMIs

#383 Thomas-Michiels opened 6 months ago
1
Question about put pattern and internal reads together to analyse

#382 Dkaaaaa opened 7 months ago
3
Question - about the result of kept_barcodes_binned.txt.BCUMIstats.txt

#381 Dkaaaaa opened 7 months ago
3
Using demultiplexed BAM files output from zUMIs with Picard Tools

#380 seifudd opened 7 months ago
1
Failed to open filtered.tagged.unmapped.bam

#379 aduntslusine opened 8 months ago
1
Mapping error at .tmpMap//tmp.test2.*.SJ.out.tab'

#378 aliibarry opened 8 months ago
5
Error in alldt[[i]][[2]] : subscript out of bounds

#377 MohamedAbdalfatah opened 8 months ago
3
Processing RNA-Seq data with UMIs from SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian

#376 seifudd closed 7 months ago
2
function 'strsplit': object 'GE' not found

#375 yangmean opened 9 months ago
4
How to only demultiplex raw reads (not mapped reads) using zUMIs

#374 ytang0831 opened 9 months ago
3
additional sequences

#373 ljy-sys opened 9 months ago
4
"More reads than allowed for the memory limit"

#372 gevro closed 10 months ago
1
running merge_demultiplex has index reads without R1/R2, leading to "ERROR! Fastq files are not in the same order"

#371 leoforster closed 9 months ago
2
Error in the counting stage

#370 russellxie opened 10 months ago
1
Starting zUMIs

#369 ISIDORAPA opened 10 months ago
1
Problems in mapping Smart-Seq3 data

#368 JinsyWang closed 10 months ago
4
Example of dual index Smart-seq3

#367 russellxie closed 10 months ago
2
[Feature Request] Adding PIPSeq barcode detection

#366 mbassalbioinformatics opened 11 months ago
1
EXITING because of fatal PARAMETERS error: sjdbOverhang <=0 while junctions are inserted on the fly with --sjdbFileChrStartEnd or/and --sjdbGTFfile

#365 hxyyxh opened 12 months ago
1
Is there a way to overwrite the STAR parameter --outSAMunmapped ?

#364 TatevikJ closed 1 year ago
4
BUG: segmentation fault during STAR mapping

#363 LJK1991 opened 1 year ago
0
Update fqfilter_v2.pl - Fix problem with multiple whitespaces in read-IDs

#362 darichter87 opened 1 year ago
0
database or disk is full

#361 gevro opened 1 year ago
3
Unable to recognize a combination of multiple barcode sequences

#360 shangyf-stu closed 1 year ago
3
UMI-collapsed BAM

#359 gevro opened 1 year ago
3
'strsplit': object 'GE' not foundBUG

#358 gevro opened 1 year ago
13
Error in fread(paste0(opt$out_dir, "/zUMIs_output/", opt$project, "kept_barcodes_binned.txt"))

#357 shangyf-stu closed 1 year ago
3
[E::hts_open_format] Failed to open file "NA" : No such file or directory

#356 officialprofile closed 1 year ago
10
What should the file content of "barcode_file: null" in line 64 of file zUMIs.yaml be?

#355 WXY-Belief closed 1 year ago
2
Error in eval(bysub, parent.frame(), parent.frame()) : object 'XC' not found Calls

#354 PeggySze closed 1 year ago
4
Question about multimapping reads

#353 MartaBenegas closed 1 year ago
5
An error was encountered while running zUMIs(v2.9.7d)

#352 shangyf-stu closed 1 year ago
7
Smart-seq-3 data subsets systematically fail after counting due to chunking

#351 Romain-B closed 1 year ago
1
Parameters related to Multimapping genes count

#350 zmf0621 closed 1 year ago
1
Pipeline QC metrics

#349 royfrancis closed 1 year ago
2
Rscript header for merge_demulitplexed_fastq.R

#348 idot opened 1 year ago
0
Can skip filtering and restart a failed run from the mapping stage?

#347 Ni-Ar closed 1 year ago
5