User: O.rka

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O.rka110
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Posts by O.rka

<prev • 145 results • page 1 of 15 • next >
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Comment: C: Randomly got the following error: CRITICAL: Error executing: kneaddata_bowtie2_d
... 2nd part: 07/15/2019 09:18:53 PM - kneaddata.utilities - INFO: Total memory = 252.185920715 GB 07/15/2019 09:18:53 PM - kneaddata.utilities - INFO: Available memory = 249.285884857 GB 07/15/2019 09:18:53 PM - kneaddata.utilities - INFO: Free memory = 234.216808319 GB 07/15/2019 09: ...
written 3 days ago by O.rka110
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Randomly got the following error: CRITICAL: Error executing: kneaddata_bowtie2_discordant_pairs but all the files before look fine?
... **Does anyone know what this could be? I've never gotten this error before and I've used kneaddata a lot.** (base) -bash-4.1$ cat metagenome_output/31-PE-N718S517-1_S12/preprocessing/kneaddata.log 07/15/2019 09:18:46 PM - kneaddata.knead_data - INFO: Running kneaddata v0.7.2 07/15/20 ...
assembly written 3 days ago by O.rka110
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Comment: C: fastq-dump timeout exhausted error
... What does --split-3 do? ...
written 27 days ago by O.rka110
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Comment: C: fastq-dump timeout exhausted error
... Wait... how does this affect when I just need to download a SRA record using fastq-dump w/ my current version? ...
written 27 days ago by O.rka110
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What tool can compute SNPs from a set of assemblies and output the SNPs into a dataframe?
... I have several assemblies all from the same bacterial strain. I want to do a SNPs analysis but **I'm having trouble finding tools that will do this and output the data into a dataframe of SNPs by position.** I have the fasta files for each assembly along with the shotgun genomic reads that went in ...
assembly written 5 weeks ago by O.rka110
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Answer: A: How To Merge Gff Files
... I know you probably figured this out since it was asked 6 years ago but I ended up using gffcompare in 2019 (for anyone else looking for this): https://ccb.jhu.edu/software/stringtie/gffcompare.shtml It worked really well. For installation: conda create --name gffcompare_env -c bioconda gf ...
written 5 weeks ago by O.rka110 • updated 5 weeks ago by WouterDeCoster40k
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Comment: C: Can any long read assemblers incorporate both nanopore and pacbio reads in the s
... I didn’t realize how similar this question was as I was writing it. Thank you for answering this. I’m going to try out the suggestions in your answer once I can get everything installed. ...
written 6 weeks ago by O.rka110
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Comment: C: Can any long read assemblers incorporate both nanopore and pacbio reads in the s
... My apologies, when I started writing this question it seemed different and then it slowly turned into the last question as I added more text. I will try not to do this again. ...
written 6 weeks ago by O.rka110
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How to extract best-hit reads from merged sam file with multiple hits per read?
... I have multiple sam files that I would like to merge. The only problem is that I may have instances where there will be multiple hits per read. Is there a way to use sam tools or any other software for removing these “duplicate” hits based on some criteria such as highest score? Also, my usage ...
alignment written 6 weeks ago by O.rka110
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Comment: C: Can any long read assemblers incorporate both nanopore and pacbio reads in the s
... I'm doing a `flye` run for the nanopore data right now. It wasn't able to handle both at the same time. It also required a `--genome-size` which is difficult since this is de-novo. ...
written 6 weeks ago by O.rka110

Latest awards to O.rka

Popular Question 24 days ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Can you assemble with merged paired end reads and unmatched reads as "single end
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Scholar 3 months ago, created an answer that has been accepted. For A: Can you assemble with merged paired end reads and unmatched reads as "single end
Centurion 4 months ago, created 100 posts.
Popular Question 5 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Popular Question 7 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 9 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Scholar 9 months ago, created an answer that has been accepted. For A: Can you assemble with merged paired end reads and unmatched reads as "single end
Popular Question 11 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 11 months ago, created a question with more than 1,000 views. For Most up-to-date Gene Ontology [GO] analysis?
Great Question 14 months ago, created a question with more than 5,000 views. For How to tell bloodtype from SNPs data?
Popular Question 15 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 19 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Supporter 2.3 years ago, voted at least 25 times.
Popular Question 2.4 years ago, created a question with more than 1,000 views. For How to tell bloodtype from SNPs data?
Student 2.9 years ago, asked a question with at least 3 up-votes. For Most up-to-date Gene Ontology [GO] analysis?

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