User: javanokendo

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Posts by javanokendo

<prev • 13 results • page 1 of 2 • next >
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enrichKEGG and ridgplot from differential analysis gene data
... I have done the differential analysis using DEseq2 and I would like to plot the ridgeplot and enrichKEGG using clusterProfiler package. The package required the entrez gene ID and my result object contain gene symbols. I have tried to `# this translates the Gene from MSfragger to something enrichgo ...
rna-seq written 3 months ago by javanokendo0
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Comment: C: enhanced volcano plot
... I have tried to extract the gene counts from BAM file using featureCounts and I keep on getting an error: "address (nil), cause 'memory not mapped". I have tried to run this both on HPC and on my local machine and I get this error. I have a total of 20 BAM files and I used the following command' ...
written 3 months ago by javanokendo0 • updated 3 months ago by Kevin Blighe66k
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enhanced volcano plot
... I am trying to visualize the volcano plot with the *EnhancedVolcano* plot package and the plot looks strange and I do not know what is causing this problem. I sent my data to the sequencing facility and they just gave me the BAM files and I do not know which version of the mouse reference genome pl ...
R enhancedvolcano rna-seq written 3 months ago by javanokendo0 • updated 3 months ago by zx87549.7k
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Comment: C: VCF output when merging with bcftools merge
... Hey can you post the full command you used to solve this problem? ...
written 5 months ago by javanokendo0
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Comment: C: Warning: Could not find FASTA file /home/praveenkumarr/rice_default/bwt/genome/g
... copy `genome.fa` to the directory containing the `indexed` genome with the same indexbase name ...
written 5 months ago by javanokendo0
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Comment: C: TopHat installation error
... This works for me...thanks ...
written 5 months ago by javanokendo0
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Converting SJ.out.tab from STAR aliner to junction.bed
... How can I convert for example T042BLSJ.out.tab output from STAR aligner to junction.bed which is similar to the tophat `junction.bed` output. I have tried the following code but it does not work: `awk {'if($4=="2") print "chr"$1"\t"$2-$9"\t"$3+$9"\tJUNC000"NR"\t"$7+$8"\t-\t"$2-$9"\t"$3+$9"\t255,0,0\ ...
alignment rna-seq written 5 months ago by javanokendo0
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Comment: C: Error: Could not find Bowtie 2 index files (GRCh38.*.bt2l)
... This option worked for me also. ...
written 5 months ago by javanokendo0
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Comment: C: Custome database creation from RNAseq dataset for proteomics database search hel
... Thanks this worked for me and I really appreciate it ...
written 5 months ago by javanokendo0
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Comment: C: Custome database creation from RNAseq dataset for proteomics database search hel
... I have done the alignment with the star aligner and I got my BAM files sorted by coordinates. ...
written 5 months ago by javanokendo0

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