no error raise but get empty results

[UronicAcid]

Hi, I'm running example case using both RNA-seq and DNA-seq.

python /path/to/REDItoolDnaRna.py \
-i  /path/to/rna.bam \
-j  /path/to/dna.bam \
-o  /path/to/my_output \
-f  /path/to/reference.fa

It returned:

Pysam version used: 0.19.0
Script time --> START: 23/06/2022 15:41:38
Analysis ID: 863990752
Analysis on 1 regions.
Started analysis on region: chr21:1-48129895
Job completed for region: chr21:1-48129895
Merging Tables.
Results saved on /gpfs/share/home/2101111835/tools/REDItools-1.2.1/testREDItools/my_output/DnaRna_863990752/outTable_863990752
Script time --> END: 23/06/2022 15:41:43

But I got empty output

(reditools) [2101111835@wm1-login01 ~/tools/REDItools-1.2.1]$cat /path/to/my_output/DnaRna_863990752/outTable_863990752
Region	Position	Reference	Strand	Coverage-q30	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage-q30	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency

[UronicAcid]

I'm using REDItools v1.2.1

[zhoudongke]

I'm using REDItools v1.2.1

excuse me？Have you solved this problem? I got a same empty result...

[evchambers]

Does the chromsome annotation in your reference file match your bams? Sometimes the 'chr' annotation at the start may not be there depending if the data is ensembl/UCSC

[Cp0728]

嗨，我正在使用 RNA-seq 和 DNA-seq 运行示例案例。

python /path/to/REDItoolDnaRna.py \
-i  /path/to/rna.bam \
-j  /path/to/dna.bam \
-o  /path/to/my_output \
-f  /path/to/reference.fa

它返回：

Pysam version used: 0.19.0
Script time --> START: 23/06/2022 15:41:38
Analysis ID: 863990752
Analysis on 1 regions.
Started analysis on region: chr21:1-48129895
Job completed for region: chr21:1-48129895
Merging Tables.
Results saved on /gpfs/share/home/2101111835/tools/REDItools-1.2.1/testREDItools/my_output/DnaRna_863990752/outTable_863990752
Script time --> END: 23/06/2022 15:41:43

但是我得到了空的输出

(reditools) [2101111835@wm1-login01 ~/tools/REDItools-1.2.1]$cat /path/to/my_output/DnaRna_863990752/outTable_863990752
Region	Position	Reference	Strand	Coverage-q30	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage-q30	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency

I wonder if you have solved the problem

[Cp0728]

I had the same problem

[Cp0728]

I'm using REDItools v1.2.1

excuse me？Have you solved this problem? I got a same empty result...

I wonder if you have solved the problem
I had the same problem

[AnnaTanada]

I am also having the same problem. Did you manage to solve it?

[AnnaTanada]

I am also having the same problem. Did you manage to solve it?

I actually solved it. The problem is in the reference file. It seems that the newer versions (or at least the one I downloaded from GENCODE, release 49) have two fields in the header, like:

">chr1 1
NNNNNNNNNNNNNNN... "etc

Apparently, REDItools does not handle well the second column(in this case, 1 (this number seems to be a repetition of the chromosome number). So I just created a copy of the reference without this second column, like:

">chr1
NNNNNNNNNNNNNNN... "etc

And now it works fine! And now I have my results and not an empty outTable file.