User: John

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John210
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Posts by John

<prev • 140 results • page 1 of 14 • next >
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Comment: C: How to download mm10 GTF file with the gene id and gene name using UCSC table br
... I can't see anything! thanks ...
written 10 weeks ago by John210
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How to download mm10 GTF file with the gene id and gene name using UCSC table browser?
... Hi, what is the parameters I should put to download the same format GTF file like the first line of GTF file below, for mm10 ? chr1 unknown exon 3214482 3216968 . - . gene_id "Xkr4"; gene_name "Xkr4"; p_id "P14345"; transcript_id "NM_001011874"; tss_id "TSS25485"; I can download this format us ...
alignment rna-seq ucsc written 10 weeks ago by John210 • updated 10 weeks ago by Luis Nassar360
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Comment: C: What % of rRNA contamination is acceptable?
... I used featurecounts to count only exons, still the same genes are showing up as DE genes. Do you think the problem is only in library prep (fragmentation)? or The low number of reads (due to rRNA contamination? My question is Will I get good coverage If I do deep sequencing with the same library ...
written 11 weeks ago by John210
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Comment: C: What % of rRNA contamination is acceptable?
... Here is the screen shot! first three samples are Condition A, Second three samples are condition B. Kat6a is upregulated in Condition B (with log2FC=0.83, padj<0.01 shown by DESEQ2). I don't know why it is aligned to intronic regions. Because the sample is ribosome bound RNA. Thanks ![5'][1] ...
written 11 weeks ago by John210
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Comment: C: What % of rRNA contamination is acceptable?
... Thanks, I looked at them in IGV. > if the transcripts are fragmented incorrectly you may end up with coverage from one end (5' or 3' only). This is not a problem. ...
written 11 weeks ago by John210
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How to get actual alignment % from STAR?
... Hi Is this formula right to calculate actual alignment percentage of my RNA seq data? I want to find out the reads mapped only to annotated genes, my sample is from Ribosome bound RNA, so I would not have introns, I want to exclude rRNA alignments from the percentage alignment. Alignment % ...
R rna-seq written 11 weeks ago by John210 • updated 27 days ago by Biostar ♦♦ 20
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Comment: C: What % of rRNA contamination is acceptable?
... Yes it works! Thanks ...
written 11 weeks ago by John210
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Comment: C: What % of rRNA contamination is acceptable?
... Got it thanks. Then I should call it pairwise comparison between two condition with three replicates each. ...
written 11 weeks ago by John210
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Comment: C: What % of rRNA contamination is acceptable?
... I have control and treatment, 3 samples each. They are not paired! P.s they’re not passive aggressive dots. Biostar didn’t allow me to comment without certain number of characters. I really appreciate everyone in the forum for helping each others! Thank you for trying to help me! ...
written 11 weeks ago by John210
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Comment: C: What % of rRNA contamination is acceptable?
... Three replicates....................... ...
written 12 weeks ago by John210

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For How to make clusters in heat map using ggplot2?
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Great Question 9 weeks ago, created a question with more than 5,000 views. For BWA MEM vs BOWTIE2 , which is best?
Popular Question 4 months ago, created a question with more than 1,000 views. For How to make clusters in heat map using ggplot2?
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Great Question 6 months ago, created a question with more than 5,000 views. For how to sum up the columns to remove the duplicated row names in RSEM output?
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Popular Question 23 months ago, created a question with more than 1,000 views. For How to get --transcript-to-gene-map in RSEM?
Popular Question 23 months ago, created a question with more than 1,000 views. For bwa mem has more MAPQ values as 0 and 60
Popular Question 23 months ago, created a question with more than 1,000 views. For how to sum up the columns to remove the duplicated row names in RSEM output?
Popular Question 23 months ago, created a question with more than 1,000 views. For converting paired end reads to single end, is this a good idea?
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