User: tianleivv

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tianleivv20
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Posts by tianleivv

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Clinvar vs Snpedia vs DbSNP
... Try ANNOVAR, which combine many databases. And its website has the descriptions of the databases: http://annovar.openbioinformatics.org/en/latest/user-guide/filter/ ...
written 8 months ago by tianleivv20
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Answer: A: Modern software for whole genome alignment visualization
... Have you tried Circos (http://circos.ca/)? ...
written 9 months ago by tianleivv20
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Answer: A: Volcano Plot Making
... It depends on what kind of data you are using. For microarray data, I suggest limma package in R, and for RNA-Seq data I suggest DESeq2. Both of them can give you pvalues and fold changes for volcano plot. ...
written 9 months ago by tianleivv20
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Comment: C: Run featureCounts with Gencode GTF
... "Overlap between reads and features" section at webpage: http://bioinf.wehi.edu.au/featureCounts/ ...
written 9 months ago by tianleivv20
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Answer: A: Run featureCounts with Gencode GTF
... I read through featureCounts and found that: "A read is said to overlap a feature if at least one read base is found to overlap the feature. For paired-end data, a fragment (or template) is said to overlap a feature if any of the two reads from that fragment is found to overlap the feature. By defau ...
written 9 months ago by tianleivv20
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Run featureCounts with Gencode GTF
... I want to extract transcriptomic reads from BAM file, I do this using featureCounts software with Gencode GTF annotation, which include annotation from both ENSEMBL and HAVANA. Will this bias my results? For example, HIST1H2BK has two exons annotated inENSEMBL and one exon annotated in HAVANA as fol ...
rna-seq written 9 months ago by tianleivv20
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Comment: C: STAR ENCODE option
... Thanks h.mon! Why did you say RSEM can use the information from multi-mapped reads to provide more accurate count estimates? Do you have any references for this? ...
written 16 months ago by tianleivv20
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STAR ENCODE option
... Hi, I am using STAR to align my RNA-seq data. I found in ENCODE options: the max number of multiple alignments allowed for a read is 20 (i.e. --outFilterMultimapNmax 20). Why it was not set as 1 to include only unique mapped reads for downstream analysis? Thanks! Lei ...
rna-seq written 16 months ago by tianleivv20 • updated 16 months ago by h.mon21k
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Comment: C: STAR mapped more reads to transcriptome
... Hi Chris, Thanks for your reply! I am actually following the ENCODE STAR+RSEM pipeline ([https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh][1]). I think no matter how I ran STAR, it should filter the reads equally for these mapped to transcriptome and genome. Thus, rea ...
written 17 months ago by tianleivv20 • updated 17 months ago by h.mon21k
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STAR mapped more reads to transcriptome
... Hi, I am following ENCODE pipeline to analyze my RNA-Seq data. However, STAR gives me more reads in the Aligned.toTranscriptome.out.bam compared to the Aligned.sortedByCoordinate.bam, which means it aligned more reads to transcriptome rather than genome. This is beyond my understanding. Did anyone ...
rna-seq written 17 months ago by tianleivv20

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Scholar 9 months ago, created an answer that has been accepted. For A: Run featureCounts with Gencode GTF

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