User: JJ

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JJ470
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3 years, 6 months ago
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Posts by JJ

<prev • 157 results • page 1 of 16 • next >
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RNAseq recommendations / terms read pairs vs. reads for paired end experiments
... Hi, [Encode][1] recommends 10 to 25M reads per sample but have used single end data. So that would mean 10 to 25M **read pairs** per sample for paired end experiments, right? I appreciate the advice. Thanks! [1]: https://www.ncbi.nlm.nih.gov/pubmed/24319002 ...
rna-seq written 8 weeks ago by JJ470 • updated 8 weeks ago by Amar630
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Answer: A: Do all samples in SRA have a corresponding sample in BioSample?
... I have accessed many public datasets and all of them have a BioSample ID, an experiment ID and run ID(s). Many but not all have a secondary sample ID which links to GEO. ...
written 3 months ago by JJ470
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Comment: C: Confusing RNA-seq Alignment Stats (HISAT2 & Qualimap)
... Thanks for the link - I understand the HISAT2 results - my question was more regarding the Qualimap results and if the `Total number of alignments / Number of secondary alignments` is too high. Having said that I also get similar results for human Encode samples. ...
written 3 months ago by JJ470
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Comment: C: Confusing RNA-seq Alignment Stats (HISAT2 & Qualimap)
... Thanks for your input. I just wanted to make sure as the `Total number of alignments / Number of secondary alignments` seems very high but the % of multi mappers appears to be ok for me. ...
written 3 months ago by JJ470
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Comment: C: Confusing RNA-seq Alignment Stats (HISAT2 & Qualimap)
... The reads are 100bp long and paired-end ...
written 3 months ago by JJ470
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6 follow
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Confusing RNA-seq Alignment Stats (HISAT2 & Qualimap)
... I am confused about the alignment stats I am getting and I really hope someone can explain them to me! So I've used HISAT2 with default parameters using the grch38_tra index available. The results that HISAT2 is reporting back to me look fine to me. See below for an example, where I have an alignm ...
rna-seq written 3 months ago by JJ470 • updated 3 months ago by yztxwd290
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Comment: C: TCGA CNV data - immensely different results depending on data source
... Thanks for your input!! > From what I understand, the data on the GDC itself (which TCGAbiolinks > uses) is just the segmented calls that have been called via Circular > Binary Segmentation. Try to think of it as a pseudo-raw form of copy > number (technically, it is just that because t ...
written 5 months ago by JJ470
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TCGA CNV data - immensely different results depending on data source
... Dear all, I am looking into genes of interest affected by CNVs using TCGA data. I am very confused about the immensely different results I get depending on the data source I use: The GDC data portal (also available via TCGAbiolinks R package) provides a simple data.frame (genes / patients with -1 ...
genome tcga cnv written 5 months ago by JJ470
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Comment: C: Pathway analysis with co-variates for RNA-seq data
... will do - thanks so much! ...
written 10 months ago by JJ470
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Comment: C: Pathway analysis with co-variates for RNA-seq data
... thanks so much for this pointer! ...
written 10 months ago by JJ470

Latest awards to JJ

Student 4 months ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Popular Question 5 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 6 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 9 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 9 months ago, created a question with more than 1,000 views. For Is there a tool that sorts gtf files?
Popular Question 9 months ago, created a question with more than 1,000 views. For SNP calling using cancer cell lines
Popular Question 9 months ago, created a question with more than 1,000 views. For Public strand-specific RNA-seq data for human tissues
Popular Question 9 months ago, created a question with more than 1,000 views. For RSeQC Output from infer_experiment.py - what does it mean?
Popular Question 9 months ago, created a question with more than 1,000 views. For TCGA data - GDC data portal vs. Firebrowse
Popular Question 13 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Student 15 months ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Popular Question 16 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 16 months ago, created a question with more than 1,000 views. For Is there a tool that sorts gtf files?
Popular Question 16 months ago, created a question with more than 1,000 views. For Clustering data - data transformation (log2) highly improves clustering but why?
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Popular Question 19 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 19 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
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Student 21 months ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Scholar 21 months ago, created an answer that has been accepted. For A: Gene Expression data and variants from the same fastqc raw file
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Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Help in writing NGS pipeline (or: the road from fasta to vcf)

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