User: Bioinfonext

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Bioinfonext200
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Posts by Bioinfonext

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Comment: C: PCA plot with phyla abundance
... Hi Asaf, Yes I do have relative abundance at phyla level. currently I am using below phyloseq code for PCoA plot but not sure how to insert bacterial abundance in this plot at phyla level. physeqN3 = filter_taxa(physeqN2, function(x) sum(x > 5) > (0.2*length(x)), TRUE) phyloseq_prop ...
written 20 days ago by Bioinfonext200
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Comment: C: PCA plot with phyla abundance
... ok, sorry for that, I have changed above image link. ...
written 28 days ago by Bioinfonext200
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PCoA plot with phyla abundance
... Hi, could anyone please help me how to make PCoA plot with phyla abundance as shown in below link from amplicon sequencing data. ![enter image description here][1] Thanks [1]: https://i.ibb.co/ZY3yg3Y/fmicb-11-00132-g005.jpg ...
vegan R phyloseq written 28 days ago by Bioinfonext200
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Comment: C: adding gene name correspond to gene id from Ensembl (Oryza sativa / rice)
... thank you so much Kevin! ...
written 7 weeks ago by Bioinfonext200
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Comment: C: adding gene name correspond to gene id from Ensembl
... yes, I am working on rice. thanks for your help. ...
written 8 weeks ago by Bioinfonext200
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adding gene name correspond to gene id from Ensembl (Oryza sativa / rice)
... Hi, I got multiple differential expressed gene list by using DESeq2, could you please suggest how I can add the gene name to this data correspond to gene ID: BGIOSGA000001 BGIOSGA000002 baseMeanAmanRootT1 baseMeanAmanRootT2 baseMean log2FoldChange lfcSE stat pvalue padj BGIOSGA000 ...
R rna-seq written 8 weeks ago by Bioinfonext200 • updated 7 weeks ago by Kevin Blighe56k
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Comment: C: cat command to get multiple fq reads into single fastq file
... thanks you very much! ...
written 3 months ago by Bioinfonext200
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cat command to get multiple fq reads into single fastq file
... Hi, file names are like this: Root_T1_S_R8_S48_unmapped.R1.fq Root_T1_S_R9_S47_unmapped.R1.fq Root_T2_F_R2_S25_unmapped.R2.fq Root_T2_F_R3_S24_unmapped.R2.fq I need to take Multiple R1.fq and R2.fq into two separate files to run trinity for de novo assembly. I am little bit ...
rna-seq linux written 3 months ago by Bioinfonext200
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Comment: C: extract unmapped pair end read from sam files
... Hi Genomax, thanks for your all help. above command seems very confusing for me as it only generate a single fastq files if I run it on sam file as well. instead of this I am using the below three command in loop command one by one as suggest by you earlier: if I come across any issue, will let yo ...
written 3 months ago by Bioinfonext200
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extract unmapped pair end read from sam files
... Hi, I do have multiple pair end sam files. I am thinking to use below command to extract unmapped read from all sam files to bam files by using below command and after this I am trying to use reformat.sh from bbtools to extract the unmapped read pair from bam file. Is there any way to run the ref ...
samtools bbtools rna-seq linux written 3 months ago by Bioinfonext200 • updated 3 months ago by genomax80k

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