Open CarolineWits opened 10 months ago
Hi @CarolineWits,
Your command looks good, can you check the adapter is actually Illumina? How to check is described here. If you want me to check, then can you share the subset/sample of your input file?
Thank you, Arun
Hi @arunhpatil ,
Thank you so much, that seems to have worked.
My next problem (sorry I am really new to all this!), I am tryng to perform a differential expression analysis and am using the following command:
miRge3.0 -s NGS_Results/RD-ADE-840.fastq.gz,NGS_Results/RD-ADE-1001.fastq.gz,NGS_Results/RD-ASU-006.fastq.gz,NGS_Results/RD-ASU-048.fastq.gz,NGS_Results/RD-EDE-011.fastq.gz,NGS_Results/RD-EJG-061.fastq.gz,NGS_Results/RD-EJG-067.fastq.gz,NGS_Results/RD-LTH-704.fastq.gz,NGS_Results/RD-LTH-783.fastq.gz,NGS_Results/RD-OLF-050.fastq.gz -lib miRge3_Lib -on human -db MirGeneDB -o differential_Exp -a "AGATCGGAAGAGCACACGTCTGAACTCCA" -dex -mdt NGS_Results/DESmetadata.csv
I get the following warnings: Summarizing and tabulating results... /home/manager/miniconda/envs/ngsbio/lib/python3.10/site-packages/mirge/libs/summary.py:764: FutureWarning: The default value of numeric_only in DataFrameGroupBy.sum is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. df = df.groupby(['miRNA']).sum()[base_names] /home/manager/miniconda/envs/ngsbio/lib/python3.10/site-packages/mirge/libs/summary.py:769: FutureWarning: The default value of numeric_only in DataFrameGroupBy.sum is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. miRNA_df = subpdMapped.groupby(['miRNA_cbind']).sum()[base_names] Summary completed in 4.4172 second(s)
Performing differential expression...
Installing package into ‘/home/manager/R/x86_64-conda-linux-gnu-library/4.0’ (as ‘lib’ is unspecified) Error in contrib.url(repos, type) : trying to use CRAN without setting a mirror Calls: install.packages -> startsWith -> contrib.url In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘BiocManager’ Execution halted
Can you help with what I have done wrong?
Thank you, Caroline
Hi @CarolineWits,
No problem and ignore the warnings for now. miRge3.0 is looking for R packages for differentiall analysis. It tried to install the packages but couldn't. Can you install the following packages in R command line.
Type R
on the command prompt and once R session opens, you can type in the following commands:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
Then install DESeq2:
if (!require("DESeq2", quietly = TRUE))
BiocManager::install("DESeq2")
Finally, ggplot for graphical assistance:
install.packages('ggplot2')
To test it has worked, type:
library(DESeq2)
library(ggplot2)
Once you all these installed type q()
and you can choose to save y
or no n
when prompted.
This will be one time installation only and you can then run miRge3.0.
Thank you, Arun
Hi, I am new to both NGS analysis and using linex. I have tried installing mirge3.0 onto my linex VM and wanted to try rum my analysis. I used the following input: miRge3.0 -s NGS_Results/RD-ADE-1001_S2_L001_R1_001.fastq.gz,NGS_Results/RD-ADE-840_S1_L001_R1_001.fastq.gz -lib miRge3_Lib -on human -db mirgenedb -o output_dir -bam -a illumina
I got the following error file: Summarizing and tabulating results... Traceback (most recent call last): File "/home/manager/miniconda/envs/ngsbio/bin/miRge3.0", line 10, in
sys.exit(main())
File "/home/manager/miniconda/envs/ngsbio/lib/python3.10/site-packages/mirge/main.py", line 166, in main
summarize(args, workDir, ref_db, base_names, pdMapped, sampleReadCounts, trimmedReadCounts, trimmedReadCountsUnique)
File "/home/manager/miniconda/envs/ngsbio/lib/python3.10/site-packages/mirge/libs/summary.py", line 744, in summarize
subpdMapped['miRNA_cbind'] = subpdMapped[['exact miRNA', 'isomiR miRNA']].apply(lambda x: ''.join(x), axis = 1)
File "/home/manager/miniconda/envs/ngsbio/lib/python3.10/site-packages/pandas/core/frame.py", line 3968, in setitem
self._set_item_frame_value(key, value)
File "/home/manager/miniconda/envs/ngsbio/lib/python3.10/site-packages/pandas/core/frame.py", line 4123, in _set_item_frame_value
raise ValueError(
ValueError: Cannot set a DataFrame with multiple columns to the single column miRNA_cbind
Can you assist? Thank you