l-modolo / tetools Goto Github PK

Hi @l-modolo!

We got a request to include your tools into https://usegalaxy.eu.
Are you planning to update the tools and maintain them? I have seen that the do not use conda packages and also don't have any tests defined.

Thanks,
Bjoern

I run TEDIFF and i´m watching this message:
Error: ncol(countData) == nrow(colData) is not TRUE
Execution halted

Hi,
Really basic question... I didn't get the relationship between the fasta file with the copies and the rosette file.

Hello,

This is my command line:
Rscript ~/Software/TEtools/TEdiff.R --args --FDR_level=0.05 --count_column=2 --count_file=\"TEcount_Midgut_0hpi_vs_mock\" experiment_formula=\"sample:replicat:condition\" --sample_names=\"Midgut_0hpi_mock:r1:mock,Midgut_0hpi_mock:r2:mock,Midgut_0hpi_mock:r3:mock,Midgut_0hpi:r1:infected,Midgut_0hpi:r2:infected,Midgut_Ohpi:r3:infected\" --outdir=\"RNAseq/TEtools\" --htmlfile=\"TEdiff_Midgut_0hpi.html\"

I get this error message:
Error in if (main_factor[i] != main_factor[j]) { :
argument is of length zero
Execution halted

I looked at TEdiff.R more into details and I saw that the line main_factor = levels(variables[,1]) returns NULL. Indeed, variables[,1] is not a factor. I can fix it by replacing it by levels(as.factor(variables[,1])) or by unique(variables[,1]) but I do not understand why in my case variables[,1] is not a factor whereas it obviously supposed to be a factor. I am wondering whether I did somtehing wrong or whether it could be a version problem (I have R v4.0) that would not make this variable a factor by default anymore.

To note, I also had a warning message due to the same factor problem:
In DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors

Thank you,

Héloïse Muller

Hi Laurent

I am trying to run the TEdiff.R. I am using the command like this:
"Rscript TEdiff.R --args --FDR_level=0.05 --count_column=2 --count_file=Check.count2 --experiment_formula=population:type --sample_names=population1:type1,population1:type2"
The error is:
"[1] "./TEdiff"
Error in eval(expr, envir, enclos) : object 'Check.count2' not found
Calls: eval -> eval
Execution halted"

I guess it is not able to recognise the count_file. I have the count_file "Check.count2" in the same directory where the R script is. If I am using the command in a wrong way. Please let me know what I am doing wrong here.

Thanks

Hello,
I am trying to run TEcount.py for single end RNAseq reads, however there is an error I receive that I am not sure what it is refer to (please see below).
Thanks,
Martina

Command: :
python3 /data/MB998/HepC_Uwe/TEtools-master/TEcount.py -rosette ROSETA_final -column 2
-TE_fasta /data/MB998/HepC_Uwe/TEtools-master/All_Repeat_sequences_2.fa -bowtie2 -count Count_result_ALL_ALIGN -RNA Marc_M38_HFLC_DMSOMOCK_D35_24h.fastq.gz Marc_M42_HFLC_DMSOHCV_D35_24h.fastq.gz Marc_M49_HFLC_DMSOMOCK_D73_24h.fastq.gz Marc_M52_HFLC_DMSOHCV_D73_24h.fastq.gz Marc_M62_HFLC_DMSOMOCK_D75_24h.fastq.gz /data/MB998/HepC_Uwe/Marc_M66_HFLC_DMSOHCV_D75_24h.fastq.gz

ERROR LOG:
counting Marc_M38_HFLC_DMSOMOCK_D35_24h.fastq.gz...
./alignment/Marc_M38_HFLC_DMSOMOCK_D35_24h.fastq.sam
building index
/data/MB998/LUNG_CANCER/TEtools-master/bowtie2/bowtie2-build -f /data/MB998/HepC_Uwe/TEtools-master/All_Repeat_sequences_2.fa /data/MB998/HepC_Uwe/TEtools-master/All_Repeat_sequences_2.fa.index2
Traceback (most recent call last):
File "/data/MB998/HepC_Uwe/TEtools-master/TEcount.py", line 557, in
args.insert_size)
File "/data/MB998/HepC_Uwe/TEtools-master/TEcount.py", line 445, in from_fastq
self.__mapping_index()
File "/data/MB998/HepC_Uwe/TEtools-master/TEcount.py", line 395, in __mapping_index
run_cmd(self.procs, bowtie_cmd)
File "/data/MB998/HepC_Uwe/TEtools-master/TEcount.py", line 89, in run_cmd
procs.append(Popen(shlex.split(command), shell=False, stdout=PIPE, stderr=PIPE, bufsize=1))
File "/home/mb998/lib/python3.7/subprocess.py", line 756, in init
restore_signals, start_new_session)
File "/home/mb998/lib/python3.7/subprocess.py", line 1499, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)

Tecount file is generated without colnames, I send you my file, i have one sample and i wrote: TEdiff.R --args --FDR_level=0.05 --count_column=2 --count_file="resultados_H1Rep1.out" experiment_formula="H1Rep1" --sample_names="H1Rep1" --outdir="Resultados_TEDIFF" --htmlfile="Resultados_TEDIFF_FILE"
I don´t know if this is ok

HEllo again!
I run TECOUNT in my cluster, i watch that sam file is building with paired 1. My command is
TEcount.py -rosette /mnt/home/users/pab_001_uma/b12loroc/dict_pos_ele_tipo_clase_transposon.table.txt -column 2 -TE_fasta /mnt/home/users/pab_001_uma/b12loroc/Hsap38.geve.nt_v1.fa -count resultadosprostata -paciente1_tumor_paired_1_.fastq paciente2_tumor_paired_1_.fastq paciente3_tumor_paired_1_.fastq paciente4_tumor_paired_1_.fastq paciente1_sano_paired_1_.fastq paciente2_sano_paired_1_.fastq paciente3_sano_paired_1_.fastq paciente4_sano_paired_1_.fastq -RNApair paciente1_tumor_paired_2_.fastq paciente2_tumor_paired_2_.fastq paciente3_tumor_paired_2_.fastq paciente4_tumor_paired_2_.fastq paciente1_sano_paired_2_.fastq paciente2_sano_paired_2_.fastq paciente3_sano_paired_2_.fastq paciente4_sano_paired_2_.fastq

I don´t understand what do you want to say with rossette file, is an extension? RSD file?, how do i make this file?

--Hi,

is there a script or a program to generate rosette file, because i don't know
how to generate it .

thank you --

Hello,

I'm new to NGS analysis and am interested in looking at RTE activity in RNAseq data from d. melanogaster. I'm not sure how to generate the rosette file - for instance, can I use information on flybase to make it (http://flybase.org/static_pages/downloads/bulkdata7.html) and if so, could you provide guidance on how?

Thanks!