User: newbie

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newbie90
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Posts by newbie

<prev • 101 results • page 1 of 11 • next >
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Comment: C: Interpretation of two PCA plots
... Thanks for the answer. I understand that they are still similar, may I know why they are mirror images? ...
written 5 hours ago by newbie90
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Interpretation of two PCA plots
... Hi, I am working with a cancer type dataset. There are in total 250 samples. All these samples are classified into 6 groups. And I plotted a PCA plot with `Gencode Protein coding genes` and it looks like below: ![enter image description here][1] Similarly, I also plotted a PCA with only `Gencode ...
pca rna-seq clustering written 6 hours ago by newbie90 • updated 6 hours ago by swbarnes28.9k
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Comment: C: How to get the output on multiple files into one file in sbatch script?
... Thanks a lot...it looks fine now. ...
written 7 days ago by newbie90
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Comment: C: How to get the output on multiple files into one file in sbatch script?
... Can you please show me how to do that? ...
written 7 days ago by newbie90
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How to get the output on multiple files into one file in sbatch script?
... Hi, I have 120 `sorted.bam` files. I would like to check the strandedness of each sample. Whether unstranded or stranded. All 120 sorted.bams are in this directory `/data/bams` For that, I kept all the sample names in the `samples.txt` file. And I started using a shell `sbatch` script like below ...
rseqc slurm sbtach strand rna-seq written 7 days ago by newbie90
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Comment: C: Why there are low assigned reads in featureCounts output and different outputs f
... I have 600 fastq.gz files. Could you please show me one example how to use `SortMeRNA` on .fastq.gz file please. thanq ...
written 21 days ago by newbie90
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Comment: C: Why there are low assigned reads in featureCounts output and different outputs f
... In my command I haven't used `-t`. So it should also count all the lncRNAs also. ...
written 21 days ago by newbie90
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Comment: C: Why there are low assigned reads in featureCounts output and different outputs f
... I have data from 300 tumor samples. And for all I see that genomic origin of reads are higher in intronic region. ...
written 21 days ago by newbie90
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Comment: C: Why there are low assigned reads in featureCounts output and different outputs f
... I see that higher intronic mapping rate is see with rRNA removal. Here wee used Ribo Zero tool kit. Equal distribution of reads mapping to intronic, exonic and intergenic regions suggests that there is DNA contamination. I got this information Fromm here [rna-seq QC tutorial][1] same seen here too [ ...
written 21 days ago by newbie90
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Why there are low assigned reads in featureCounts output and different outputs for quality checks?
... I'm using rnaseq data (paired-end and strand-specific) which is rRNA depleted with Ribo-Zero Gold rRNA Removal Kit. I observed that most number of reads are intronic (genomic origin), which is due to Ribo-Zero. I did the alignment with `Hisat2`. Quality check of the alignment was done with `RNA-seq ...
reads alignment featurecounts qualimap rna-seq written 21 days ago by newbie90 • updated 21 days ago by rpolicastro2.0k

Latest awards to newbie

Centurion 7 days ago, created 100 posts.
Popular Question 5 weeks ago, created a question with more than 1,000 views. For How to get read counts on transcript level using featurecounts?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Differential analysis show different results with edgeR and in box plot with t-test
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Popular Question 6 months ago, created a question with more than 1,000 views. For How to filter low expressed genes based on TPM expression?

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