User: CAnna

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CAnna20
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Posts by CAnna

<prev • 28 results • page 1 of 3 • next >
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Answer: C: State of processing in ENA, metaHIT samples
... Thanks for your advice. Following this I emailed the authors who would confirm: *"All fastq files correspond to processed reads, i.e. filtered to remove both low quality reads and contaminant human sequences. I suppose that the terminology heterogeneity comes from the fact that these metagenomic sa ...
written 2.6 years ago by CAnna20
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Comment: C: State of processing in ENA, metaHIT samples
... Thanks for your reply. I see those names on the downloaded files. In the link you sent, if you click on the link for the submitted fastq ('Fastq file 1'), the name of the file is: MetaHIT-MH0001_081026.**rmHuman.rmHost**.&.fq.gz'. I either get files with 'rmHuman.rmHost' or 'clean.rmHost' depend ...
written 2.6 years ago by CAnna20
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State of processing in ENA, metaHIT samples
... Hi, I am downloading samples from the metaHIT project (metagenomes from faecal samples). From the paper, it is said that the 'raw illumina reads are deposited at ENA with accession number ERP003612', so [there][1] However when downloading the files (submitted fastq) the naming is of the form 'Meta ...
metahit filtering ena written 2.6 years ago by CAnna20
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Answer: A: BBMap genome indexing - java issue?
... Arg, I figured it out. For the sake of potential beginners having this kind of issue, this was related to my shell script. If you do specify a value for -Xmx it needs to be less than the amount of virtual memory that you reserve for your job. In my case I had reserved 30GB of vmem, so should set -X ...
written 2.8 years ago by CAnna20 • updated 2.8 years ago by GenoMax94k
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Comment: C: BBMap genome indexing - java issue?
... Ha, this is tricky, the thing is that I do not have any output/error to suggest what is wrong. I don't think it is a memory issue since maxvmem if I recall says how much memory has been used at max and this says 0. Looks like it did not run at all? ...
written 2.8 years ago by CAnna20
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Comment: C: BBMap genome indexing - java issue?
... Thanks for your reply Yes I am specifying -l h_vmem=24G on the job scheduler I am using Java 8 (java/jdk/1.8.0) And the log file of the job scheduler is here (if this is what you meant?) qname eddie hostname node2c03.ecdf.ed.ac.uk group eddie_users owner ...
written 2.8 years ago by CAnna20
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Comment: C: What stage of pre-processing in EBI data?
... Great, Thanks for the tools recommendation! ...
written 2.8 years ago by CAnna20
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BBMap genome indexing - java issue?
... Hi, I want to remove human contaminants from gut metagenomes. For this I am using BBMap. The first step is to index the contaminant genome (human genome). I am following the exact procedure as described [here][1], which I cross validated by finding the same commands described on other pages ([biost ...
indexing java bbmap written 2.8 years ago by CAnna20
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What stage of pre-processing in EBI data?
... Hi, I am trying to figure out the necessary pre-processing steps before using sequencing data retreived from online databases. I work with metagenomes from Huaman gut microbiome. I figured out that the main three steps for this type of data are: 1) Identify and mask Human reads 2) Remove duplica ...
preprocessing raw data filtering written 2.8 years ago by CAnna20
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Comment: C: paired-end read: background + practical question - Strainphlan pipeline
... Thanks! This is very helpful. ...
written 3.0 years ago by CAnna20

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Scholar 2.8 years ago, created an answer that has been accepted. For A: BBMap genome indexing - java issue?

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