User: c.e.chong

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c.e.chong10
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Posts by c.e.chong

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Bowtie database of all bacterial and fungal complete genomes
... Thank you for your reply! I have considered getting representatives for broad classes. My plan was to use CD-HIT to remove redundancy once I had downloaded all of the bacterial and fungal complete genomes, do you think this is the best method? I have used Kraken2 but I want to access the bam fil ...
written 12 days ago by c.e.chong10
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Bowtie database of all bacterial and fungal complete genomes
... Hi all, I would like to create a database of all the bacterial and fungal complete genomes in the RefSeq database to map all of my Metagenome samples to it. Does anyone know if this is possible? The manual states that you have to input a comma separated list of fasta files to build the database, ...
bowtie2 metagenomics mapping shotgun written 4 weeks ago by c.e.chong10
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Comment: C: Kraken2 to Phyloseq
... Thank you for your reply, is there a preferred method for generating a table of the number of reads mapped to each contig from the bam file? Is this the same as calculating coverage? Also is DeSeq recommended to find taxonomic differences between samples/groups of samples? Or more the genes within ...
written 4 weeks ago by c.e.chong10
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Comment: C: Kraken2 to Phyloseq
... I have previously mapped my reads to databases made from the contigs of each sample when using anvio to bin my samples. Would these bam files contain the sufficient information to do the comparisons? To use kraken to find out what the differential contigs are should I input the concoct contig bins I ...
written 5 weeks ago by c.e.chong10
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Kraken2 to Phyloseq
... Hi all, I am quite new to Metagenomics and how to statistically analyse my data. I have run kraken2 to taxonomically profile my assembled metagenomics samples. I have three different disease state groups and I would like to see if there are any statistical differences between them. I decided to ...
R kraken shotgun metagenomics statistics written 5 weeks ago by c.e.chong10 • updated 5 weeks ago by Asaf6.1k
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Comment: C: Java error message when using BBDuk
... That worked! Such a simple fix!! Thank you very much! ...
written 4 months ago by c.e.chong10
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Comment: C: Java error message when using BBDuk
... That worked! Such a simple fix!! Thank you very much! ...
written 4 months ago by c.e.chong10
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Comment: C: Java error message when using BBDuk
... Yes, my files are already trimmed for adapters I am now doing a quality trim. I tried with the lower number of RAM and threads and got this error: Exception in thread "main" java.lang.NullPointerException at shared.Parser.parseTrim(Parser.java:333) at jgi.BBDuk.(BBDuk.java:176) ...
written 4 months ago by c.e.chong10 • updated 4 months ago by genomax69k
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Comment: C: Java error message when using BBDuk
... I run validateFiles on my fastq files and the output was "Error count 0" ...
written 4 months ago by c.e.chong10
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Java error message when using BBDuk
... Hi all, I am trying to run BBDuk to quality trim and filter my illumina whole genome sequences. I have used this program before and haven't had any problems. However when I run the command: bbduk.sh -Xmx80g in1=17198wC1_Sample_3_1_trimmed.fastq in2=17198wC1_Sample_3_2_trimmed.fastq out1=~/c ...
genome java bbduk qc bbtools written 4 months ago by c.e.chong10 • updated 4 months ago by genomax69k

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