User: Carlo Yague

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Carlo Yague3.9k
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Posts by Carlo Yague

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Comment: C: Why I see very high mapping percentage, Is this normal or anything wrong in gene
... 2.What are those genes without read counts ? Sometimes very small ncRNA such as miRNAs and pirRNAs are in the annotation but not well captured in total RNA-seq. So for those classes of RNA, it should be ok to have 0 read counts. On the other hand, if you have 0 read count for most protein coding gen ...
written 1 hour ago by Carlo Yague3.9k
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Comment: C: bedtools getfasta (how to get only cds coding sequence)
... You need to merge the DNA sequence of your cds before translating it, it will fix the reading phase problem. ...
written 3 hours ago by Carlo Yague3.9k
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Comment: C: bedtools getfasta (how to get only cds coding sequence)
... just create the file yourself. Something like: awk '$3 == "CDS" {print $0}' run_augustus_0035.gff.out > run_augustus_0035_cds_only.gff ...
written 2 days ago by Carlo Yague3.9k
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Answer: A: bedtools getfasta (how to get only cds coding sequence)
... I think that bedtools getfasta will not parse your gff3 file based on [cds -> mRNA] relationship. Therefore you get either the sequence cds by cds, or from start to end of the mRNA (including introns). The frame shift caused by the introns would explain the number of stop codons you find. This w ...
written 2 days ago by Carlo Yague3.9k
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Comment: C: Why difference in Hisat2 and bamqc from qualimap results?
... > But could you please tell me how this total number of reads and total > number of alignments are different? Because for one read, there can be more than one alignment : `(41.44%) aligned concordantly >1 times` > And could you also tell me how u calculated the above percentages. 100 ...
written 6 days ago by Carlo Yague3.9k
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Comment: C: Why difference in Hisat2 and bamqc from qualimap results?
... The percentage of unmapped reads (compared to the total number of reads) is 30.53%. The percentage of unmapped reads (compared to the total number of alignments in the bam file) is 12%. ...
written 6 days ago by Carlo Yague3.9k
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Comment: C: Why difference in Hisat2 and bamqc from qualimap results?
... Both metrics are right. In your bam file, you have 88% of mapped reads. From your input reads, only 69% are mapped (once or more than once). The mutlitple alignments are causing the difference ...
written 6 days ago by Carlo Yague3.9k
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Answer: A: Ribo-seq couts are more than RNA-seq count
... We can imagine that some RNAs are in low absolute concentration in your RNA-seq total sample, but that they are translated with high efficiency and end up enriched in the Ribo-seq sample. Because they are enriched, they would account for higher proportions of the library, so I don't find your result ...
written 9 days ago by Carlo Yague3.9k
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Answer: A: How to compare coverage eveness of two whole genome sequencing runs of the same
... There is a rather simple tool designed to do exactly what you want: [cnv-seq][1]. Its a bit old but rather straightforward. I used it in the past and as far as I remember, it was easy to use and it made [nice figures][2]. [1]: https://dx.doi.org/10.1186%2F1471-2105-10-80 [2]: https://www.biost ...
written 9 days ago by Carlo Yague3.9k
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Comment: C: HISAT2 for loop shell scripting
... In addition `$RNA_REFS_DIR` is not defined. `$RNA_DATA_DIR/${i}_*_R1_001.fastq` is also weird. Why do you use a wildcard here ? I think your code is a bit messed up. You should probably test your loop first with something like: for i in $(ls *.fastq | rev | cut -c 22- | rev | uniq) do ...
written 10 days ago by Carlo Yague3.9k

Latest awards to Carlo Yague

Popular Question 23 days ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Scholar 25 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 8 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 3 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 3 months ago, created a question with more than 1,000 views. For Intron-aware coverage for paired-end RNA-seq data.
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 6 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 8 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 9 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 9 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 11 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 13 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene

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