User: Bioinfo

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Bioinfo170
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Posts by Bioinfo

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How to separate protein-coding and non-coding in gtf file
... Hi, In a gtf file I see "gene_type" column with different names like below. Among those names what all come under non-coding, protein_coding, lncRNA? 3prime_overlapping_ncRNA IG_C_gene IG_C_pseudogene IG_D_gene IG_J_gene IG_J_pseudogene IG_V_gene IG_V_pseudogene ...
gtf noncoding proteincoding rna-seq lncrna written 4 days ago by Bioinfo170 • updated 4 days ago by Nicolas Rosewick6.2k
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Comment: C: Why difference in Hisat2 and bamqc from qualimap results?
... Thank you very much. I guess there is a typo in ur comment. It should be 100% - 88% = 12%. ...
written 6 days ago by Bioinfo170
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Comment: C: Why difference in Hisat2 and bamqc from qualimap results?
... Thank you. But could you please tell me how this total number of reads and total number of alignments are different? And could you also tell me how u calculated the above percentages. ...
written 6 days ago by Bioinfo170
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Comment: C: Why difference in Hisat2 and bamqc from qualimap results?
... Ok. And how can I get unmapped reads percentage? 88% of mapped reads is once? ...
written 6 days ago by Bioinfo170
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Why difference in Hisat2 and bamqc from qualimap results?
... Hi, I'm using hisat2 for aligning reads to the genome. For a few samples I see some differences by using hisat2 and bamqc from qualimap. Hisat2 output: 37317546 reads; of these: 37317546 (100.00%) were paired; of these: 14771091 (39.58%) aligned concordantly 0 times 708 ...
bamqc qualimap rna-seq hisat2 written 6 days ago by Bioinfo170 • updated 5 days ago by Biostar ♦♦ 20
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Comment: C: convert human gene names to ensembl ID
... yes it is R version problem. Thank you ...
written 11 days ago by Bioinfo170
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Comment: C: convert human gene names to ensembl ID
... Hi, I have an error. library(ensembldb) library(EnsDb.Hsapiens.v79) genes=c("CEACAM8", "CXCL1","CXCL2","CXCL5","CXCL8","MPO","ARG1","FCGR3B", "CCL20","CCL2","IL1RN","IL10","TGFB1","IL6","CCL3","CCL4") genes(EnsDb.Hsapiens.v79, filter=list(GenenameFilter(genes),GeneIdFil ...
written 12 days ago by Bioinfo170
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Comment: C: Samples with same TCGA barcode in TCGA data
... Thank you very much for the information. ...
written 12 days ago by Bioinfo170
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Comment: C: Samples with same TCGA barcode in TCGA data
... Thanks but I have a doubt. Please check this one. TCGA-A6-2684-01A-01R-1410-07 TCGA-A6-2684-01A-01R-A278-07 TCGA-A6-6650-01A-11R-A278-07 TCGA-A6-6650-01A-11R-1774-07 TCGA-A6-2674-01A-02R-A278-07 TCGA-A6-2674-01A-02R-0821-07 TCGA-A6-3809-01A-01R-A2 ...
written 13 days ago by Bioinfo170
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Comment: C: Samples with same TCGA barcode in TCGA data
... Thanks for the information. You mean in the above example I need to select "TCGA-A6-6650-01A-11R-A278-07" ? plate number A278? ...
written 13 days ago by Bioinfo170

Latest awards to Bioinfo

Popular Question 23 days ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Teacher 24 days ago, created an answer with at least 3 up-votes. For C: Sample names for TCGA data from GDC-legacy archive
Scholar 25 days ago, created an answer that has been accepted. For C: Sample names for TCGA data from GDC-legacy archive
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 4 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 5 months ago, created a question with more than 1,000 views. For How to build Hisat2 index for human genome (GRCh37 )?
Centurion 6 months ago, created 100 posts.
Supporter 10 months ago, voted at least 25 times.

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