User: espop23

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espop2360
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London
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4 years, 2 months ago
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Posts by espop23

<prev • 33 results • page 1 of 4 • next >
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Job: DADA2/R Programmer Needed for One-Time Job
... Need an experienced R-programmer, with experience with DADA-2 and optimising pipelines for biological data. Have a pipeline that is not delivering to species-level as desired. Need script to be refined to ensure high accuracy, precision, and greater detection. You much have experience with micro ...
R dada2 job microbiome written 6 days ago by espop2360
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Anyone with experience in Phyloseq in R?
... Hi, I looking for someone to please help me with using phyloseq in R, since I am having trouble working with it on some files. Please write if you can help! Thank you! ...
R phyloseq qiime written 3.3 years ago by espop2360 • updated 2.3 years ago by Bioinformatics_NewComer320
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Formating picrust output for LEfSe
... I have the table generated from picrust: "matrix_type": "sparse","matrix_element_type": "float","shape": [328, 152],"data": [[0,0,23.0],[0,2,12.0],[0,5,252.0],[0,7,387.0],[0,8,53.0],[0,9,2.0],[0,11,936.0],[0,12,319.0],[0,13,330.0],[0,14,2.0],[0,15,116.0],[0,16,729.0] ... and need some help re ...
microbiome lefse picrust excel written 3.3 years ago by espop2360
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Is Flash with default settings fine?
... Hello, I ran Flash on numerous fastq samples, going on to use them in QIIME, and generating a biom file. However, I have now realised that I used default settings and did not use -M 300 & -t 8, so my maximum overlap was much lower. Can someone please give me some insights into how significant ...
flash biom fastq qiime written 3.4 years ago by espop2360
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Comment: C: Trouble with Split libraries in Qiime
... It was the file, fixed it, thanks. ...
written 3.5 years ago by espop2360
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Automating Qiime Split Libraries
... I have 100s of *joined.fastq.extendedFrags.fastq*files that I want to run split libraries on. It works when I do this for each file: split_libraries_fastq.py -i 03142103_joined.fastq.extendedFrags.fastq --sample_id 03142103 -o split_lib_03142103/ -m solo\ mapping\ files//03142103_mapping.txt - ...
libraries split terminal qiime written 3.5 years ago by espop2360 • updated 3.5 years ago by genomax73k
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Answer: A: Qiime Error in Split Libraries
... As in /Users//Documents/Data/High merged/44881102_mapping.txt ? I tried that and it comes up with the same error... Any suggestions? ...
written 3.5 years ago by espop2360
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Qiime Error in Split Libraries
... Hello, I am trying to use split libraries in qiime. The mapping files are in the folder I write, but I am getting this error and am not sure why: *split_libraries_fastq.py -i High\ merged/*_merged.fastq --sample_id 44881102 -o split_lib_44881102/ -m 44881102_mapping.txt --barcode_type 'not-b ...
libraries split qiime written 3.5 years ago by espop2360
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Joining multiple paired end-reads in qiime
... Hello, I am trying to join multiple paired end-reads in qiime. Essentially, I have a folder called teaser that has all my forward and end reads, which all start with sample and then have numbered identifiers. I have used the following code: *$ multiple_join_paired_ends.py -i teaser/sample* -o joi ...
paired sequence qiime written 3.5 years ago by espop2360
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Comment: C: Automating Flash Sequence Joins
... I ran the exact line you last wrote, and got a merged fastq for each input file. There is only one out.extendedFrags.fastq - is this as expected? (I am new to FLASH, apologies for confusion) ...
written 3.5 years ago by espop2360

Latest awards to espop23

Popular Question 3.3 years ago, created a question with more than 1,000 views. For Qiime Error in Split Libraries
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Joining multiple paired end-reads in qiime
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Automating Flash Sequence Joins
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How do you find the percentage of reads contaminated by rRNA?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How can CAGE and RNA-Seq data complement each other?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Unzipping bz2 files
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Automating Qiime Split Libraries
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Parsing GTF file - Help!
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Formating picrust output for LEfSe

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