transcript samsa2 issues

transcript / samsa2

SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.

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issues

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Loosing too many reads after Pear step

#85 abithapr closed 1 month ago
1
Information regarding New available databases - Refseq and SEED database

#84 meghahs closed 4 months ago
2
Lisakmalins

#83 transcript closed 5 months ago
0
More flexible filename handling

#82 lisakmalins closed 5 months ago
0
error while running run_DESeq_stats.R

#81 rachel1898 closed 5 months ago
5
update

#80 yjiakang closed 1 year ago
1
Clean up unmodified bash scripts

#79 edoyango closed 1 year ago
1
test_of_master_script.py

#78 spencerlong1 closed 1 year ago
2
error standardized_DIAMOND_analysis_counter.py

#77 arianlundberg opened 1 year ago
4
Error in R-analysis step

#76 dhananyashunmugam closed 1 year ago
2
issue with get_normalized_count_table.R

#75 Malabady opened 1 year ago
0
Error in DIAMOND_analysis_counter.py

#74 McKSal opened 1 year ago
1
Sequencing depth differs between experimental and control

#73 mweberr closed 2 years ago
1
Issue with colors in 'make_combined_graphs.R

#72 mbeckm01 opened 2 years ago
1
Combine step 5 outputs from different samples

#71 Vincev454 opened 2 years ago
1
Error with R script: DESeq_stats.

#70 pauvic opened 2 years ago
11
full_database_download.bash which versions?

#69 agavriilidou closed 2 years ago
1
Error correction (package_installation.bash and full_database_download.bash, issues66)

#68 EugeneKim76 closed 2 years ago
0
modify full_database_download.bash issue66

#67 EugeneKim76 closed 2 years ago
0
About full_database_download.bash

#66 EugeneKim76 closed 2 years ago
8
Error running DIAMOND_subsystems_analysis_counter.py

#65 eKariuki-sleepy opened 2 years ago
9
counter scripts using blast format 6 with salltitles

#64 bartns opened 3 years ago
0
Help with script

#63 ghost closed 3 years ago
0
AttributeError: module 'time' has no attribute 'clock'

#62 ARW-UBT closed 3 years ago
5
Update DIAMOND_subsystems_analysis_counter.py

#61 jjkoehorst closed 3 years ago
0
Header parsing using blast format 6 with salltitles

#60 jjkoehorst opened 3 years ago
1
Working with Archaea

#59 gaofeng-ni closed 3 years ago
3
SEED results for a selected organism

#58 elcega closed 3 years ago
1
Error in DIAMOND_analysis_counter.py

#57 mweberr opened 3 years ago
3
Checkpoint TRIMMO

#56 mweberr closed 3 years ago
1
Read duplication

#55 mweberr closed 3 years ago
1
volcano_plot.R

#54 benbechade closed 3 years ago
1
Slow run time and issue with running run_DESeq_stats.R

#53 Anto007 closed 3 years ago
2
How to deal with the same proteins with slightly different names from the RefSeq_bac database?

#52 memoll opened 3 years ago
2
Combining the concatenated (unassembled) forward and reverse reads with the assembled reads

#51 memoll closed 3 years ago
1
Assigning NAs as 1 might bias alpha diversity estimates?

#50 paulsalachan closed 4 years ago
2
DIAMOND_analysis_counter.py issue

#49 marco91sol closed 4 years ago
2
Error with DIAMOND Database

#48 mweberr closed 4 years ago
1
How does the Refseq database supplied with samsa2 script differ to the one available online

#47 mradz19 closed 2 years ago
4
How DIAMOND_analysis_counter.py works?

#46 Shicheng-Guo closed 4 years ago
2
'Bacteria' in the result of combined_graphs_unified.R

#45 Shicheng-Guo closed 4 years ago
3
SAMS2 bash script for 16S rRNA pipeline

#44 Shicheng-Guo opened 4 years ago
1
How much difference is expected between master_script and preserving_unmerged.sh

#43 Shicheng-Guo closed 4 years ago
1
Estimate microbial diversity with rRNA

#42 Shicheng-Guo closed 4 years ago
1
database option in DIAMOND_analysis_counter.py

#41 Shicheng-Guo closed 4 years ago
2
High number of hypothetical proteins

#40 mradz19 closed 4 years ago
1
Running the included R scripts to generate figures

#39 mradz19 closed 4 years ago
7
Help with scripts

#38 mradz19 closed 4 years ago
2
Parsing of genus/species names

#37 mattjmeier opened 4 years ago
1
SAMSA2 wrapper for Galaxy

#36 mushalallam opened 4 years ago
1