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YangLab / CIRCexplorer2

circular RNA analysis toolset
http://circexplorer2.readthedocs.org/
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Is it possible to do circexplorer2 denovo using other aligners?? #38

Closed sambhav2mishra closed 4 years ago

sambhav2mishra commented 4 years ago

Kindly suggest me any alternative to perform denovo. when i run it manually using tophat2 or circalign, it shows me the following error:

[2019-09-17 16:53:51] Beginning TopHat run (v2.1.0)

[2019-09-17 16:53:51] Checking for Bowtie Bowtie version: 1.2.3.0 [2019-09-17 16:53:51] Checking for Bowtie index files (genome).. [2019-09-17 16:53:51] Checking for reference FASTA file Warning: Could not find FASTA file /userdata/Dramaresh/fastq_dir/GMA_alignment/bowtie1_index/bowtie1_index.fa [2019-09-17 16:53:51] Reconstituting reference FASTA file from Bowtie index Executing: /userdata/Dramaresh/tools/bowtie-1.2.3-linux-x86_64/bowtie-inspect /userdata/Dramaresh/fastq_dir/GMA_alignment/bowtie1_index/bowtie1_index > /userdata/Dramaresh/fastq_dir/GMA_alignment/tophat_fusion/tmp/bowtie1_index.fa [2019-09-17 16:55:26] Generating SAM header for /userdata/Dramaresh/fastq_dir/GMA_alignment/bowtie1_index/bowtie1_index [2019-09-17 16:55:30] Preparing reads left reads: min. length=19, max. length=151, 12158285 kept reads (20688 discarded) Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places [2019-09-17 16:58:36] Mapping left_kept_reads to genome bowtie1_index with Bowtie [FAILED] Error running bowtie: Error while flushing and closing output terminate called after throwing an instance of 'int'

Your suggestions/solution will be appreciated by our lab. Thanks sambhav

iichelhadi commented 3 years ago

I got the same error. Have you found a solution. I tried STAR but at a certain step downstream cufflinks is necessary and my understanding is that it requires tophat.

sambhav2mishra commented 3 years ago

I got the same error. Have you found a solution. I tried STAR but at a certain step downstream cufflinks is necessary and my understanding is that it requires tophat.

Try using bowtie v1.0.0 (works with specific version)

iichelhadi commented 3 years ago

I got the same error. Have you found a solution. I tried STAR but at a certain step downstream cufflinks is necessary and my understanding is that it requires tophat.

Try using bowtie v1.0.0 (works with specific version)

I used STAR because bowtie1 doesn't work for me with the same error as above. Couldn't find a solution for that either