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sdparekh
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zUMIs
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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BUG Input files perceived as NULL while they exist (checked multiple times)
#405
ulyssebaruchel
opened
1 month ago
1
BUG: split cannot open path error
#404
YinCY123
opened
1 month ago
1
One or more of your executables were not found. Please check back.
#403
Johnny3333
opened
1 month ago
0
/genomeParameters.txt: No such file or directory
#402
lysurgeon
opened
2 months ago
0
Can zUMIs be used for DNA-seq data alignment?
#401
zhober
opened
2 months ago
0
zUMIs on cDNA with varied length
#400
HaikuoLi
opened
3 months ago
0
Bugs in pigz and samtools when using zUMIs 2.9.7
#399
ShoIwama
closed
3 months ago
1
zUMIs.sh starver and staridxver
#398
lishuangshuang0616
opened
4 months ago
0
Problem with STAR version
#397
joannaslotaczarny
opened
4 months ago
0
zUMIs didn't create gene_names.txt in the output folder
#396
JinsyWang
closed
5 months ago
1
Calculating TPM or FPKM
#395
gevro
opened
6 months ago
0
BUG
#394
nhu-github
opened
7 months ago
1
R error during counting step before demultiplexing.
#393
dfmoralesb
opened
7 months ago
0
Error in using zumis to analyse transposon
#392
ROund-code
opened
7 months ago
0
error in using zUMIs to processing smartseq3 data
#391
GGboy-Zzz
opened
9 months ago
0
Cannot get the example data from Google Drive
#390
RoseMary93
opened
9 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
9 months ago
0
Error with Corrrecting UB tags when working with large sample size
#388
kvn95ss
opened
10 months ago
0
aligning to multiple genomes?
#387
brennaremick
closed
9 months ago
1
The .git/objects/pack file is so huge
#386
bioinfotec
opened
10 months ago
1
[main_cat] ERROR: input is not BAM or CRAM
#385
Thomas0194
closed
10 months ago
2
Beginning zUMIs from unmapped, tagged, corrected BAM out of fqfilter_v2.pl
#384
biobenkj
closed
11 months ago
7
Issues while starting zUMIs
#383
Thomas-Michiels
opened
11 months ago
1
Question about put pattern and internal reads together to analyse
#382
Dkaaaaa
opened
11 months ago
3
Question - about the result of kept_barcodes_binned.txt.BCUMIstats.txt
#381
Dkaaaaa
opened
1 year ago
3
Using demultiplexed BAM files output from zUMIs with Picard Tools
#380
seifudd
opened
1 year ago
1
Failed to open filtered.tagged.unmapped.bam
#379
aduntslusine
opened
1 year ago
1
Mapping error at .tmpMap//tmp.test2.*.SJ.out.tab'
#378
aliibarry
opened
1 year ago
5
Error in alldt[[i]][[2]] : subscript out of bounds
#377
MohamedAbdalfatah
opened
1 year ago
3
Processing RNA-Seq data with UMIs from SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian
#376
seifudd
closed
1 year ago
2
function 'strsplit': object 'GE' not found
#375
yangmean
opened
1 year ago
4
How to only demultiplex raw reads (not mapped reads) using zUMIs
#374
ytang0831
opened
1 year ago
3
additional sequences
#373
ljy-sys
opened
1 year ago
4
"More reads than allowed for the memory limit"
#372
gevro
closed
1 year 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
1 year ago
2
Error in the counting stage
#370
russellxie
opened
1 year ago
1
Starting zUMIs
#369
ISIDORAPA
opened
1 year ago
1
Problems in mapping Smart-Seq3 data
#368
JinsyWang
closed
1 year ago
4
Example of dual index Smart-seq3
#367
russellxie
closed
1 year ago
2
[Feature Request] Adding PIPSeq barcode detection
#366
mbassalbioinformatics
opened
1 year 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
1 year 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
4
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
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