Directories are empty when running differential expression modes (a similar problem)

[mrb20045]

Hi Actually, I faced the same issue as discussed before "Directories are empty when running differential expression modes ".

I tried different approaches to fix it. I fell that the problem is related to diff_exp_read_in.py line 57: diff_exp = pd.read_csv(conditions_file,sep='\t',index_col=0)

Here, conditions_file is read but it seems to be mistake and output of the differential expression has to be inputted. Also, I could not find the results of differential expression here. Could you please take a look.

Regards

[sjroth]

Hi,

As requested earlier, please show your command and stdout (this is standard for programming so I recommend getting in the habit). Also, please provide the meta and comparisons files. I cannot "take a look" if you don't provide these resources.

Best, Sam

[mrb20045]

To run differential Expression with Read-In Information mode the below code used and log files is attached. It is worth noting that everything is OK but no file is generated.

ARTDeco -mode diff_exp_read_in -layout PE -stranded False -skip-bam-summary -meta-file metadata.txt -comparisons-file conditiones.txt -bam-files-dir bamfiles -gtf-file ../0_GTF/modified_genes.gtf -chrom-sizes-file ../0_GTF/genome.chrom.sizes -cpu 60 -read-in-threshold 0 -read-in-fpkm 0.15 -log2FC 2 -pval 0.05

_log_DE-Read-In.txt

To run DoG Differential Expression mode the below code used and log files is attached.

ARTDeco -mode diff_exp_dogs -layout PE -stranded False -skip-bam-summary -meta-file metadata.txt -comparisons-file conditiones.txt -cpu 60 -bam-files-dir bamfiles

_log_DE-DOG.txt

Meat and conditions files are attached as follow:

conditiones.txt metadata.txt

[sjroth]

Thank you! One last request: can you give me the output of the "head" command for your reformatted gene expression file?

[mrb20045]

head of the files:

[Uploading gene.exp.raw.txt…]()

[sjroth]

I don't need the entire file. I just need the column names.

[mrb20045]

ID Length Sample_1 Sample_10 Sample_11 Sample_12 Sample_2 Sample_3 Sample_4 Sample_5 Sample_6 Sample_7 Sample_8 Sample_9

[sjroth]

Hmmm... Nothing looks off to me. Can you upload the meta.reformatted.txt and comparisons.reformatted.txt? Otherwise, I suggest deleting those files and the diff_exp* folders and re-running. I am currently refactoring the package because of issues with rpy2 in general. This is easily the most brittle part of the pipeline.

[mrb20045]

I ran the code several times in different ways. meta.reformatted.txt and comparisons.reformatted.txt are correct.

After several tries I found that it is because of rpy2. First, I downgraded my rpy2 to 2.9.4 but it could not fix the problem.

Can you provide an R code for differential expression analysis for read_in ?

I did DE_DOGs analysis but could not understand the analysis for DE read_in.

[sjroth]

I understand your frustration. You uploading these files will help me identify any bugs during my update. Please remember that I'm here to help. Here are the files I want: gene.exp.raw.txt meta.reformatted.txt comparisons.reformatted.txt

If I cannot identify an issue, I will return analyzed output with the code I use.

[mrb20045]

Here you go,

gene.exp.raw.txt meta.reformatted.txt comparisons.reformatted.txt

[faleevz]

Hi there, still facing similar issues- any update in regards to this error?

[sjroth]

I am in the midst of refactoring the code, but I am very busy with work and personal obligations.