User: Carlo Yague

gravatar for Carlo Yague
Carlo Yague2.1k
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Posts by Carlo Yague

<prev • 325 results • page 1 of 33 • next >
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Answer: A: featurecounts of Rsubread strand specific orientation options
... Stranded and reversely stranded match the A on your picture. check this [blog post][1] for more insight : A_2 = fr-firststrand = reversely stranded (the R2 read is in the same direction than the RNA fragment) A_1 = fr-secondstrand = stranded (the R1 read is in the same direction than the RNA fr ...
written 2 days ago by Carlo Yague2.1k
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Comment: C: Calculating intron coordinates from gtf/gff3
... What kind of output do you exactly want ? A toy example could help too. ...
written 18 days ago by Carlo Yague2.1k
3
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Answer: A: understanding multi-mapped reads
... > The total mapped reads from the bam file is 28250742 This is the total number of alignments, which is different than the total number of reads. Reads can have 0, 1 or more alignments. - There are 25159791-1027691=24132100 reads that map only 1 time. - There are 1027691 reads that map multi ...
written 18 days ago by Carlo Yague2.1k
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Comment: C: Number of genes
... That makes sense, thanks for clarifying. ...
written 19 days ago by Carlo Yague2.1k
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Comment: C: Number of genes
... What is a trancript unit for you ? For me it is the very definition of gene... ...
written 19 days ago by Carlo Yague2.1k
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Answer: A: RNA Seq length distribution plot
... To get the distribution of the read length from the reads mapping on tRNAs (untested) : samtools view -L tRNA.bed my_bam.bam | \ # extract the reads that map on tRNAs awk '{print length($10)}' | \ # get their length sort -n | uniq -c # get the length distribution From th ...
written 19 days ago by Carlo Yague2.1k
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Answer: A: Uneven coverage correlated with Alu sequences (and discordant read pairs) in NGS
... Hi ! I don't find this pattern very surprising given that : 1 - Alu elements are repeated sequences : a read originating from one Alu repeat can very well map to another repeat. What is the mapping quality for those reads ? This can explain the high discordant pairing rate (one read mapping to one ...
written 19 days ago by Carlo Yague2.1k
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Comment: C: Extract reads from bam based on start coordinate
... If your ultimate goal is to get the number of 5' position of reads at each genomic position, then you can try [bedtools genomecov -5][1]. EDIT : it is not a very clear question indeed. [1]: http://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html ...
written 20 days ago by Carlo Yague2.1k
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Comment: C: Calculate forward and reverse strand reads from bam
... Perhaps this can help too : [Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand][1] [1]: https://www.biostars.org/p/92935/ ...
written 24 days ago by Carlo Yague2.1k
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Comment: C: How to change depth of sequence in RNA-seq fastq files
... I think Charles clarified the issue in its last post. Indeed, downsampling in NGS is usually made at the read level, not the replicate level. Note that it can be faster and more efficient to downsample the **mapped** reads (.bam or .sam files) rather than the raw reads in order to avoid mapping mu ...
written 26 days ago by Carlo Yague2.1k

Latest awards to Carlo Yague

Scholar 17 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Commentator 26 days ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Scholar 27 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 27 days 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 9 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 9 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Scholar 3 months 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
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
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
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 5 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
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
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
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
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