User: Sam

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Sam70
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Posts by Sam

<prev • 57 results • page 1 of 6 • next >
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What could be the cause of different levels of binding in ChIP-Seq Input samples?
... In ChIP-Seq Drosophila data, there is a large difference between the Input samples. Calling peaks when one is taken as the treatment, and another as the control yields thousands of peaks. Plotting the bam files in Ngsplot reveals that after normalization, in some of the Inputs there is much more bi ...
chip-seq ngsplot written 16 days ago by Sam70 • updated 16 days ago by Carlo Yague5.2k
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Comment: C: Should the number of significantly DE genes rise with the number of SVs estimate
... From SVA manual : > The goal of the sva is to remove all unwanted sources of variation > while protecting the contrasts due to the primary variables included > in mod. This leads to the identification of features that are > consistently different between groups, removing all common sou ...
written 25 days ago by Sam70
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Comment: C: Should the number of significantly DE genes rise with the number of SVs estimate
... Clarified the question. ...
written 4 weeks ago by Sam70
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Should the number of significantly DE genes rise with the number of SVs estimated (SVA package)?
... Is there a **monotonous** relationship between the number of SVs one estimates (sva package), and the number of DE genes one should get as significant? In other words, is it true that the more SVs are used, the more DE genes should be significant? (I understand that a large number of significantly ...
sva written 4 weeks ago by Sam70
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Comment: C: Providing R1,R2 to macs2
... Also (for the sake of understanding), I was told that when the technology was worse, people merged biological replicates, when they had not enough material in them separately. What is the substantial difference between merging biological replicates, and merging R1 and R2? ...
written 6 weeks ago by Sam70
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Comment: C: Providing R1,R2 to macs2
... Thanks. Just for understanding's sake, if you don't mind : If I would use both R1 and R2 in the way suggested above, it would artificially inflate the number of fragments, considering each read as a fragment. Suppose, just as an artificial example, that there are exactly 1M pairs. So, after after ...
written 6 weeks ago by Sam70
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Comment: C: Providing R1,R2 to macs2
... bowtie ..Mus_musculus/Ensembl/GRCm38/Sequence/BowtieIndex/genome -1 Sample1_R1.fastq -2 Sample1_R2.fastq -m 1 --fr --sam -p 8 --tryhard --minins 0 --maxins 1000 --chunkmbs 2000 Sample1.sam The average percentage of the reads that failed to align (neither uniquely nor multi mapped) in each sampl ...
written 6 weeks ago by Sam70
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Providing R1,R2 to macs2
... I have paired-end ChIP-Seq data that resulted in a low amount of uniquely mapped reads. When mapping the reads PE, only a small percentage maps concordantly. I want to check whether the reads give some biological sense. For that, I thought of mapping SE, taking the condition with the best statist ...
macs2 chip-seq written 6 weeks ago by Sam70
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Clarifying the meaning of Bowtie2's default alignment mode (noob question)
... The default alignment mode of bowtie2 is "search for multiple alignments, report the best one". As far as I understand this means that secondary and supplementary alignments will not be reported. Which means that > samtools view -f2304 sample_bowtie2Mapped.bam | wc -l will always yield zero. ...
bowtie2 written 6 weeks ago by Sam70 • updated 6 weeks ago by Istvan Albert ♦♦ 86k
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Comment: C: Should discodant alignments be retained in ChIP-Seq experiments?
... These tutorials are indeed single-read. Silly me. ...
written 6 weeks ago by Sam70

Latest awards to Sam

Scholar 3 months ago, created an answer that has been accepted. For A: What is the right way to convert probe names from Brainarray Custom CDF to Ensem
Scholar 5 months ago, created an answer that has been accepted. For A: What is the right way to convert probe names from Brainarray Custom CDF to Ensem

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