Closed NitinMandloi closed 5 years ago
Hi
Please provide me more information, such as the version of NCLscan you use, ... or you can try the "NCL_Scan5.py" in the latest version of NCLscan, put it in your project directory, and then run
> ./NCL_Scan5.py
and you can see if it works.
And about the file "result.sam", since it is the alignment of the reads mapped to the 'junction pseudo-reference', not reference genome, so it might be not possible to import "result.sam" to IGV directly.
Thanks.
Hi
I am using NCLscan_v1.3.
Thank you
Ok, Please try the new version of NCLscan! The "total number of support reads" was provided since NCLscan v1.4.
Thanks! :-)
Ok, So I should put all the files from V1.5 to V1.3 and then rerun the whole analysis???
Thank you
You may just copy two new scripts "Add_read_count.py" and "utils.py" into your project directory, and run the following command:
> ./Add_read_count.py -pj [Project_name] -tmp [Your_original_result_file] -sam [The_result_sam_file] -o [Output_file_name]
And the last three columns of the output would be the total numbers of support/junc/span reads.
Thanks.
p.s. The argument "[Your_original_result_file]" described above actually need to input the ".result.tmp" file, sorry for the unclearness!
Hi
After running the full pipeline I got fusions where no of junction reads are 1 and total no of span reads are 0. Can I report this results for my sample. Here only 1 read is supporting these fusions.
Example:
Chr Junction Coordinate Strand Gene Chr Junction Coordinate Strand Gene Intragenic (1) or intergenic (0) case Total number of all support reads Total number of junc-reads Total number of span-reads chr17 76415806 + PGS1 chr17 76411033 + PGS1 1 1 1 0 chr1 3431966 - MEGF6 chr1 36931801 - CSF3R 0 1 1 0 chr14 88471566 + GPR65 chr21 34918519 + SON 0 1 1 0 chr8 143572176 + BAI1 chr18 72914295 - ZADH2 0 1 1 0 chr9 139559237 + EGFL7 chr17 42299830 + RP5-882C2.2 0 1 1 0 chr17 29231084 - TEFM chr17 42295664 - UBTF 0 1 1 0 chr2 71766369 + DYSF chr15 45007621 + B2M 0 1 1 0
Kindly help me regarding this.
Thank you
Kindly reply...
Apart from this I would like to see my results in IGV any successions regarding that...
Hi,
NCLscan reports low false positive, so it depends on your project. :-)
Hi
After running the full pipeline I got fusions where no of junction reads are 1 and total no of span >reads are 0. Can I report this results for my sample. Here only 1 read is supporting these fusions.
Example:
Chr Junction Coordinate Strand Gene Chr Junction Coordinate Strand Gene Intragenic (1) or >intergenic (0) case Total number of all support reads Total number of junc-reads Total number of >span-reads chr17 76415806 + PGS1 chr17 76411033 + PGS1 1 1 1 0 chr1 3431966 - MEGF6 chr1 36931801 - CSF3R 0 1 1 0 chr14 88471566 + GPR65 chr21 34918519 + SON 0 1 1 0 chr8 143572176 + BAI1 chr18 72914295 - ZADH2 0 1 1 0 chr9 139559237 + EGFL7 chr17 42299830 + RP5-882C2.2 0 1 1 0 chr17 29231084 - TEFM chr17 42295664 - UBTF 0 1 1 0 chr2 71766369 + DYSF chr15 45007621 + B2M 0 1 1 0
Kindly help me regarding this.
Thank you
About the visualization, there are still no simple way to do so, but you can get the IDs of support reads from the ".result.sam" by using the event ID in ".result.tmp" as the key, and then you may use such IDs to get the original reads.
Apart from this I would like to see my results in IGV any successions regarding that...
Hi
I am running the updated version which is V1.6. I am getting following error:
Error: The requested bed file (/MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.preJS.bed) could not be opened. Exiting! Error: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS.ndx does not appear to be a valid novoindex. Code 9 Error: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS.ndx does not appear to be a valid novoindex. Code 9 ValueError: zero length field name in format ValueError: zero length field name in format Error: The requested bed file (/MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.PreJS2.bed) could not be opened. Exiting! Error: /MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.JS2.ndx does not appear to be a valid novoindex. Code 9 ValueError: zero length field name in format ValueError: zero length field name in format ValueError: zero length field name in format ValueError: zero length field name in format IndexError: list index out of range IOError: [Errno 2] No such file or directory: '/MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.result.tmp2' IOError: [Errno 2] No such file or directory: '/MGMSTAR1/SHARED/ANALYSIS/TRAIL/NCLscan_v1.3/V1.6//S12.result.tmp3'
Kindly help me resolving this.
Thank you
Regards
Hi,
Please check the "S12.preJS.bed" first, is it generated successfully?
Hi...
Yes that file is empty!!!!
It seems that the Python in your system is not 2.7.
Yes this was the problem.
If we are getting total supporting reads as 1 or 2 or 4 then will it be false positive??
What should be minimum cutoff to accept a true fusion here???
In general, 2 is an acceptable cutoff for the total supporting reads, but it still depends on your project!
Yes this was the problem.
If we are getting total supporting reads as 1 or 2 or 4 then will it be false positive??
What should be minimum cutoff to accept a true fusion here???
the file "2481_TR.JS.seq12" is empty. What is wrong? I have run the NCLscan v1.6 under linux (centos 7) on a 64-bit machine with 32 CPU cores and 512GB RAM to analysis human cancer RNA-seq paired-end data. The python is 2.7.11. The attachment is the full detail of result files. ncl_log.txt
Hi
I am using NCLscan for my RNA seq data. I am able to run the full pipeline. I got my sam and tab delimited result file. I am unable to see Total number of all support reads, Total number of junc-reads, Total number of span-reads in .result file.
Also if I want to import the sam file to IGV to just validate the results. Can I use result.sam file to IGV?
Kindly help me regarding the same.
Thank you
Regards