AfterQC
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OpenGene
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Hi! I managed to run AfterQC succesfully the first time I used it with one of my libraries with the following command line: pypy /home/pop_manuel/proyecto_transcriptoma_rhizophagus/software/AfterQC-master/after.py I tried to use the...
It may be a good idea to implement and option to remove specific sequences like overrepresented sequences, usually being rRNA or PCR artefacts; well passing these sequences in a fasta...
Hi there I am getting the following error Traceback (most recent call last): File "/Users/apple/miniconda3/envs/py27/bin/after.py", line 228, in main() File "/Users/apple/miniconda3/envs/py27/bin/after.py", line 222, in main processOptions(options) File "/Users/apple/miniconda3/envs/py27/bin/after.py", line 175,...
I would like to ask a question. Can I parse paired-end files after the process joined by AfterQC?
AfterQC is constantly counting wrong the total bases in paired end Miseq fastq reads. For example two paired end files with total bases 611,060,153 (as calculated by various programs) it...
Hi , in preprocesser.py line 498 , your code is : `if lowQual1 > self.options.unqualified_base_limit or lowQual1 > self.options.unqualified_base_limit:` I suppose the code should be : `if lowQual1 > self.options.unqualified_base_limit...
Hello, I have using afterqc with default settings to remove adapter sequences from RNA Seq read files. My original files have all the reads of uniform length. After processing with...
Hello, I have a 12 paired end files(50gb~). For each file it takes me 14hrs approx to run with native python. I read that with pypy command it runs 3...
Hi, I'm working on SRA data (SRR4292097). I get the following error `after.py specify current dir as input dir SRR4292097_R1.fastq.gz ./SRR4292097_R1.fastq.gz options: {'read1_file': './SRR4292097_R1.fastq.gz', 'read2_file': './SRR4292097_R2.fastq.gz', 'index1_file': None, 'index2_file': None,...
