Combine the results

[JunmingH]

Hi I was trying to combine the results together. since there have have issue when I integrate those bam files together. Right now I have CircCoordinates CircRNACount CircSkipJunctions LinearCount Four files for each subjects. I was wondering how could I cimbine each subjects together. using which column to match them?
Thanks!

[tjakobi]

Hi @JunmingH,

you would have to combing the different output files, into one set of files with multiple columns for each of the samples. However, the rows will be different, too, since not all circRNAs will be detect in each sample. I would recommend to try to get all sample processed by DCC in one run, possibly with -T 2 or 2 to not create too much CPU and memory load.

Cheers,
Tobias

[JunmingH]

Hi @tjakobi Tobias,

I was trying to using server to processing the data but still gave me the error,
Traceback (most recent call last):
File "/restricted/projectnb/casa/jmh/RNA-seq/circu_RNA/DCC-0.4.7/DCC/main.py", line 818, in
main()
File "DCC-0.4.7/DCC/main.py", line 254, in main
minL=options.min, strand=False, pairdendindependent=False, same=same), Input)
File "/share/pkg.7/python2/2.7.16/install/lib/python2.7/multiprocessing/pool.py", line 253, in map
return self.map_async(func, iterable, chunksize).get()
File "/share/pkg.7/python2/2.7.16/install/lib/python2.7/multiprocessing/pool.py", line 572, in get
raise self._value
IndexError: list index out of range

[tjakobi]

Could you please attach the log file of that DCC run?

[JunmingH]

samplesheet.txt
bam_files.txt
DDC2_e.txt
DDC2_o.txt
Attached is

[JunmingH]

@tjakobi Can you give me some idea for this?

[tjakobi]

Hi @JunmingH,

I am relatively sure that your command line is not correct, see the following error:

DDC2_o.txt:     => locating circRNAs (unstranded mode) [/restricted/projectnb/casa/jmh/RNA-seq/circu_RNA/script/samplesheet]
DDC2_o.txt:WARNING: File /restricted/projectnb/casa/jmh/RNA-seq/circu_RNA/script/samplesheet, line 2 does not contain all features.
DDC2_o.txt:WARNING: /restricted/projectnb/casa/jmh/RNA-seq/circu_RNA/script/samplesheet is probably corrupt.

Here the Junctions files should be scanned, not the samplesheet.

Can you please provide your complete command line?

Cheers,
Tobias

[JunmingH]

@tjakobi Hi Tobias,

Attached is~
python2 ${app_dir}/main.py @samplesheet
-D -N -R ${gtf_dir}/GRCh38_Repeats_simpleRepeats_RepeatMasker.gtf
-an ref/GRCh38/annotation/Homo_sapiens.GRCh38.95.gtf
-F -M -Nr 1 1 -fg -G -A ref/Homo_sapiens.GRCh38.dna.primary_assembly.fa
-T 2 -O /dcc_all_results/
-B @bam_files

[tjakobi]

The samplesheet and the command line look okay - however DCC seems to think there is only one input file called samplesheet.

Your command line is not the command line that DCC itself prints out, do you have the complete DCC log, i.e. DCC-2019***.log? That log file contains the actuall command line DCC sees.

Cheers,
Tobias

[JunmingH]

@tjakobi Sure,
Attached is
2019-11-24 14:54:23,207 DCC 0.4.7 started
2019-11-24 14:54:23,207 DCC command line: /jmh/RNA-seq/circu_RNA/DCC-0.4.7/DCC/main.py /jmh/RNA-seq/circu_RNA/script/samplesheet -D -N -R jmh/RNA-seq/circu_RNA/script/ref/GRCh38_Repeats_simpleRepeats_RepeatMasker.gtf -an /jmh/ref/GRCh38/annotation/Homo_sapiens.GRCh38.95.gtf -F -M -Nr 1 1 -fg -G -A /bu_brain_rnaseq/hjm_test/step_by_step/ref_RSEM/ref/Homo_sapiens.GRCh38.dna.primary_assembly.fa -T 2 -O /jmh/RNA-seq/circu_RNA/dcc_all_results/ -B /jmh/RNA-seq/circu_RNA/script/bam_files
2019-11-24 14:54:23,422 Starting to detect circRNAs
2019-11-24 14:54:23,422 Non-stranded data, the strand of circRNAs guessed from the strand of host genes
2019-11-24 14:54:23,423 started circRNA detection from file /jmh/RNA-seq/circu_RNA/script/samplesheet

[tjakobi]

Hi @JunmingH,

from the log file you can see that the actual command line is

jmh/RNA-seq/circu_RNA/DCC-0.4.7/DCC/main.py /jmh/RNA-seq/circu_RNA/script/samplesheet

While it should be

jmh/RNA-seq/circu_RNA/DCC-0.4.7/DCC/main.py @/jmh/RNA-seq/circu_RNA/script/samplesheet

The @ for the input is missing.

Cheers,
Tobias

[JunmingH]

Hi @tjakobi Tobias

Thanks for your help! It's working right now!