User: Carlo Yague

gravatar for Carlo Yague
Carlo Yague4.0k
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Posts by Carlo Yague

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Comment: C: get identical number of read1 and read2 aligned
... You can also try to use `samtools fixmate` to update mate-related flags before running `flagstats`. ...
written 6 days ago by Carlo Yague4.0k
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Comment: C: get identical number of read1 and read2 aligned
... alternatively, to extract the mapped reads whose mates are also mapped, u can use samtools view -F 12 ...
written 7 days ago by Carlo Yague4.0k
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Answer: A: extract one-side unmapped reads from sam
... > I'd like to extract from unmapped.bam only those reads where only one > side of the pair (R1 or R2) was not mapped, i.e. exclude records where > both R1 and R2 are unmapped That would be : samtools view -f 5 -F 8 Which mean that you take all read that are paired and unmapped (-f 5) ...
written 8 days ago by Carlo Yague4.0k
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Comment: C: How to assess the Fold-change significance using a t-test in R?
... To the best of my knowledge, this is not possible with just the fold change. ...
written 11 days ago by Carlo Yague4.0k
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Comment: C: bowtie2 unmapped reads
... > Based on the samtools stats, that really should give the correct > number of unmapped reads - right? It would be interesting to compare the number of unmapped reads (-F 4) and the number of not properly aligned pairs (-F 2). ...
written 12 days ago by Carlo Yague4.0k
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Comment: C: bowtie2 unmapped reads
... > However, when counting the lines in the files and dividing by four, I > get that there are 620,381,610 reads in R1 and 620,027,677 in R2... Are you counting the lines of the gzipped file ? If it is compressed, then the number of lines is not directly related to the number of reads. To make ...
written 12 days ago by Carlo Yague4.0k
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Comment: C: ChIP Seq poor mapping quality and strange fast QC result
... It won't really solve your problem, but you can try to use `samtools view -F 4` and `samtools view -f 4` to respectively extract the mapped and unmapped reads from your bam file. Then you can run FASTQC on those unmapped.bam and mapped.bam files. It might allow to better characterize the unmapped re ...
written 13 days ago by Carlo Yague4.0k
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Comment: C: ChIP Seq poor mapping quality and strange fast QC result
... Ok, that makes sense. For the IP data, it seems that this G-T bias goes further into the reads. I don't know why though, so you might need to contact the guys responsible for the sequencing. Meanwhile, you can try this: 1- trim the 9 first nucleotides of your IP as you did for your input. Is it st ...
written 14 days ago by Carlo Yague4.0k
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Answer: A: Why to remove lowly expressed genes in RNAseq
... The main reason behind the idea of discarding low count genes is to NOT test genes for which we presume a difference in expression would not be relevant. If you do less tests, then the correction for multiple testing becomes less stringent, and the overal power of your experiment increases. This con ...
written 14 days ago by Carlo Yague4.0k
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Comment: C: ChIP Seq poor mapping quality and strange fast QC result
... > Hi, you may right click on the image icon and "Open image in new tab". > This worked for me. Yes, it works now, thank you. Even from the input, the 9 first nucleotide are only G-T, which is weird. Did you use some kind of custom adapter for your library preparation ? Did you use the standar ...
written 14 days ago by Carlo Yague4.0k

Latest awards to Carlo Yague

Good Answer 17 days ago, created an answer that was upvoted at least 5 times. For A: The bed12 format
Scholar 5 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Scholar 11 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
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
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 3 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 5 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 5 months ago, created a question with more than 1,000 views. For Intron-aware coverage for paired-end RNA-seq data.
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
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 6 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 6 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 6 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 7 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
Teacher 8 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 10 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 11 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 11 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 11 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene

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