User: Carlo Yague

gravatar for Carlo Yague
Carlo Yague3.2k
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Posts by Carlo Yague

<prev • 436 results • page 1 of 44 • next >
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Comment: C: Aligning multiple fastq files in Bowtie2
... What happens if you call bowtie on the other set of fastq files ? ./bowtie2 -t -x bss -1 C55.1.fastq -2 C55.2.fastq -S C55.sam ...
written 1 day ago by Carlo Yague3.2k
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Comment: C: RNA spike-ins: Their applications and bioinformatics methods for the analysis
... Hi Devon, out of curiosity, could you elaborate on the issues with the ERCC spike-ins ? ...
written 7 days ago by Carlo Yague3.2k
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Comment: C: input for DEseq2 differential expression and multi comparisons between samples
... hint : you need to include the age in your design to answer your questions (not *condition.condition*, the actual age without the "C" or "D"). ...
written 19 days ago by Carlo Yague3.2k
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Answer: A: Is the consistency of the NGS library size important?
... I don't have a full answer to this question but since you ask for any bit of advice, here comes my two cents : - Variation in the sonication efficiency from sample to sample, even in the same batch, is not unusual. At least it happened to several people i know. They choose to throw away the sample ...
written 6 weeks ago by Carlo Yague3.2k
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Comment: C: tRNA differential expression analysis in mRNA sequencing data
... Northern blots are basically the same as southern blots except that you use RNA samples instead of DNA. Therefore, all gels and buffers must be made with RNAse free water and you should wear gloves all the time. Here is a [general protocol][1] for Northern blots. 10% acrylamide gels are the best fo ...
written 6 weeks ago by Carlo Yague3.2k
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Answer: A: tRNA differential expression analysis in mRNA sequencing data
... Hi, tRNA (and rRNA) contamination of poly-A enriched samples is expected due to their relative abondance indeed. But to compare their expression, you would need to assume that the "contamination" is the same in all your samples which is probably not true. If you want to make sure that the differenc ...
written 6 weeks ago by Carlo Yague3.2k
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Comment: C: Extract reads from bam/sam files using read id
... After trying to play with grep and a sam file (it worked but was so sloooow), I found your answer and its much faster, thx. ...
written 6 weeks ago by Carlo Yague3.2k
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Comment: C: Coverage and fragment length
... Is it paired or single end ? ...
written 6 weeks ago by Carlo Yague3.2k
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Comment: C: Parse results of predicted miRNAs
... This certainly improves the output formatting. But wy do you use `uniq -d` ? As a consequence, you ignore all miRNAs with less than two targets (such as hsa-miR-3 in this case). I would rather use `uniq` without the -d. ...
written 7 weeks ago by Carlo Yague3.2k
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Comment: C: Alingment of ~23 Mb sequences
... There is also [LASTZ][1]. According to its author : > LASTZ can perform full [human] chromosome-to-chromosome alignments in 2G of memory. [1]: http://www.bx.psu.edu/~rsharris/lastz/ ...
written 7 weeks ago by Carlo Yague3.2k

Latest awards to Carlo Yague

Scholar 6 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 9 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
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Scholar 10 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 3 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
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 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
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: The bed12 format
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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
Popular Question 6 months ago, created a question with more than 1,000 views. For Intron-aware coverage for paired-end RNA-seq data.
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 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 7 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene

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