User: espop23

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espop2360
Reputation:
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New User
Location:
Switzerland
Last seen:
2 years, 8 months ago
Joined:
3 years, 7 months ago
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Posts by espop23

<prev • 32 results • page 1 of 4 • next >
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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 2.7 years ago by espop2360 • updated 21 months 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 2.7 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 2.8 years ago by espop2360
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Comment: C: Trouble with Split libraries in Qiime
... It was the file, fixed it, thanks. ...
written 2.9 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 2.9 years ago by espop2360 • updated 2.9 years ago by genomax64k
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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 2.9 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 2.9 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 2.9 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 2.9 years ago by espop2360
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Comment: C: Automating Flash Sequence Joins
... Is there a way to create folders for each pair in the script or someway to separate the output? Since it seems the output files are being overwritten each time... ...
written 2.9 years ago by espop2360

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