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The problem of reconstruct_contig.py #13
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Hi @crystal0721 ,
-Liz |
hi Magdoll, Crystal |
Hi @crystal0721 , One possibility is to combine {Trinity} + {HQ isoforms from SMRTLink/SMRTAnalysis} into a single fasta file and run it through Cogent. After reconstruction, use the collapse script per this tutorial to collapse any redundant transcripts. The collapse script should not care if the sequence comes from Trinity or HQ. Let me know if you run into issues. --Liz |
hi Magdoll, Crystal |
Hi @crystal0721 ,
I was answering your question in how to combine (Illumina) Trinity data with PacBio HQ isoforms. The reason I suggested combining Trinity + HQ isoforms and run Cogent is to get the union of the genes the two platforms cover. Another possibility, which you have hinted, is:
The combination of {2} + {3} will then get you the combined final dataset. --Liz |
Hi @Magdoll, I also want to combine the HQ and rnaspades assembly to generate a complete transcriptome. I used the above strategy:
If I only use the HQ data, I can get the final results without any error. But 10% of the HQ sequences were ignored because of the coverage issues, is that normal? Thanks! Chen |
Hi @jayceejiao , The collapse scripts expect a certain sequence ID format that the RNA-seq data is not following. It needs to look like this:
it's looking for the "f10p0" which needs to be after the right "/" symbol. YOu can use a Python script to force RNA-seq/Trinity data to have that:
--Liz |
Hi @Magdoll, I have changed the transcript id and got the final representative transcriptome. Thanks! |
hi, Dear
when I test reconstruct_contig.py,there is a problem as follows:
reconstruct_contig.py -h
Traceback (most recent call last):
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/bin/reconstruct_contig.py", line 4, in
import('pkg_resources').run_script('Cogent==2.1', 'reconstruct_contig.py')
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/site-packages/pkg_resources/init.py", line 748, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/site-packages/pkg_resources/init.py", line 1517, in run_script
exec(code, namespace, namespace)
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/site-packages/Cogent-2.1-py2.7.egg/EGG-INFO/scripts/reconstruct_contig.py", line 301, in
args = parser.parse_args()
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 1701, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 1733, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 1939, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 1879, in consume_optional
take_action(action, args, option_string)
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 1807, in take_action
action(self, namespace, argument_values, option_string)
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 996, in call
parser.print_help()
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 2340, in print_help
self._print_message(self.format_help(), file)
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 2314, in format_help
return formatter.format_help()
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 281, in format_help
help = self._root_section.format_help()
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 211, in format_help
func(*args)
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 211, in format_help
func(*args)
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 517, in _format_action
help_text = self._expand_help(action)
File "/home/software/Cogent/software/Anaconda2/envs/anaCogent/lib/python2.7/argparse.py", line 603, in _expand_help
return self._get_help_string(action) % params
ValueError: unsupported format character ')' (0x29) at index 32
The python version is 2.7.14,could you tell be how to solove it,thank you very much.
Crystal
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