sheffield-bioinformatics-core periscope issues

sheffield-bioinformatics-core / periscope

A tool to quantify sub-genomic RNA (sgRNA) expression in SARS-CoV-2 artic network amplicon nanopore sequencing data.

GNU General Public License v3.0

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issues

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Illumina _periscope.bam output file

#52 galeoni opened 1 year ago
0
Missing {input.path} in reheader rule

#51 ThomasBaudeau opened 1 year ago
0
ORF start position does not match for every gen

#50 TimonKapischke closed 1 year ago
0
split: <filename>.sam illegal line count

#49 sekstephenson opened 1 year ago
2
Error when running search_for_sgRNA_illumina.py

#48 kjshan opened 1 year ago
1
error line 16 in search_for_sgRNA_illumina.py

#47 laurabuggiotti opened 1 year ago
2
gRNA counts for illumina data

#46 cohenp05 opened 2 years ago
1
sgRNA count is less than gRNA count

#45 pratibha-kadam closed 2 years ago
5
KeyError: 'ORF7a', Illumina reads

#44 DrownedMala closed 2 years ago
13
illumina gRNA count

#43 pratibha-kadam closed 2 years ago
8
Why is the artic package version pinned at 1.1.1?

#42 wm75 opened 2 years ago
2
Generate same ONT statistics for Illumina data

#41 Liukvr closed 2 years ago
10
failed on install python 3.6

#40 happykhan closed 2 years ago
1
snakefile error /bin/bash: bc: command not found split: invalid number of lines:

#39 Viromic opened 2 years ago
3
Error while running periscope

#38 DrownedMala closed 2 years ago
1
error “one of the commands exited with non-zero exit code; note: snakemake uses bash strict mode"

#37 quangu0925 closed 2 years ago
5
UnicodeEncodeError

#36 mbdabrowska1 opened 3 years ago
0
Add support for Qiagen primers and amplicons

#35 mbdabrowska1 opened 3 years ago
0
Bug fixes

#34 mbdabrowska1 closed 3 years ago
0
ModuleNotFoundError

#33 jwarger closed 3 years ago
0
Vanguard

#32 mbdabrowska1 closed 3 years ago
0
Fix tqdm for multiprocessing for ont and illumina

#31 mbdabrowska1 opened 3 years ago
0
Uncouple mapping threading from periscope threading

#30 mbdabrowska1 closed 3 years ago
1
Add citation file to point to genome research paper

#29 mattdmem opened 3 years ago
0
Adds midnight and V4 primers, as well as the option to provide custom primers

#28 mbdabrowska1 closed 3 years ago
0
Fixes ORF1a being called as sgRNA and updates tests for ont and illumina

#27 mbdabrowska1 closed 3 years ago
1
Add 1.2kb midnight primers

#26 mattdmem closed 3 years ago
1
Incorrect mapped_reads count for Illumina data

#25 mbdabrowska1 closed 3 years ago
1
Better discernment of actual leader/body junction, classify?

#24 mattdmem opened 3 years ago
0
Fix tests and start implementing more tests for more data types

#23 mattdmem closed 3 years ago
1
Add normalisation to ORF1ab counts

#22 mattdmem opened 3 years ago
0
Testing and optimisation for ARTIC V4 primers

#21 mattdmem closed 3 years ago
1
Incorrect sgRNA normalisation per mapped reads

#20 mbdabrowska1 closed 3 years ago
0
Resources folder fix

#19 mbdabrowska1 closed 3 years ago
0
Move over vangaurd optimisations to Illumina data

#18 mattdmem closed 3 years ago
1
ORF1ab - sgRNA being called

#17 mattdmem closed 3 years ago
1
Investigate behaviour of primer site filtering for noncanonical sgRNA

#16 mattdmem opened 3 years ago
0
Resources folder location

#15 mattdmem closed 3 years ago
0
Error in execution

#14 tmctmc123 closed 3 years ago
6
Remove human reads - Add steps to filter to only SARS-CoV-2 reads?

#13 mattdmem opened 3 years ago
1
Installation error: writing to /tmp

#12 ksw9 opened 3 years ago
1
ORFs not being tagged properly in the bam file

#11 mattdmem opened 4 years ago
0
Illumina data fails when getting coverage close to ends

#10 mattdmem closed 4 years ago
1
Normalisation of amplicon based illumina data

#9 mattdmem opened 4 years ago
3
Detect fastqs and act accordingly

#8 mattdmem closed 4 years ago
0
Classify non-canonical sgRNA according to cell paper

#7 mattdmem opened 4 years ago
0
pybedtools error - novel sub-genomic at 0

#6 mattdmem closed 4 years ago
1
Give option to process illumina data.

#5 mattdmem closed 4 years ago
1
Provide R code for plots and analysis

#4 mattdmem opened 4 years ago
3
Use spliced alignments and junction reads to quantify sgRNA

#3 mattdmem opened 4 years ago
1