User: francois

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francois10
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Posts by francois

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No reads in IGV at the positions indicated by the bed file
... I have Illumina paired-end reads. I aligned them to my reference genome then generated a bed file of my reads' positions from the bam file. I have many reads at: ` chr11_KZ115359v1_alt:87033-87183 ` However, I cannot see any read at this position on IGV. The reads were aligned to zebrafish genome ...
sequencing written 5 months ago by francois10
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Comment: C: RNAseq: What's the accurate way to test whether a set of N genes is differential
... Sure, but I believe that is a different question. Why would I not be able to specifically look a set of genes and ask whether they are down/upregulated as a set? ...
written 7 months ago by francois10
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RNAseq: What's the accurate way to test whether a set of N genes is differentially expressed?
... In RNAseq data, I want to test statistically whether a set of 17 genes are differentially expressed in a condition. I have two conditions: control treated/drug treated. My quick & dirty way of looking at it was: I computed up/downregulation vs control by simply dividing the counts in drug treate ...
rna-seq written 7 months ago by francois10 • updated 7 months ago by Devon Ryan93k
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Can I conclude anything from MiSeq primer reads?
... I am sequencing with MiSeq loci I targeted with CRISPR-Cas9. I sometimes have many paired small primer reads (see [pic attached][1]), Can I conclude anything from them? They are definitely not random, I see more often at specific loci/in some samples. Can they be hint of large deletions? [1]: htt ...
sequencing written 7 months ago by francois10 • updated 7 months ago by Friederike5.2k
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Comment: C: How to predict non-sense mediated decay from Illumina reads?
... Right, I see. It's a shame, it'd be nice data to have! ...
written 8 months ago by francois10
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Comment: C: How to predict non-sense mediated decay from Illumina reads?
... Just had a shot with a read now. I manually wrote the variant (it is just a 10bp deletion in the middle of the read). It does a pretty good job for part of it: looking up which transcript the variant will affect and calling a frameshift. I wish it would go transcribe/translate downstream in the new ...
written 8 months ago by francois10
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Comment: C: How to predict non-sense mediated decay from Illumina reads?
... Thanks. It's very helpful; but I think the variant caller will not do the job I need. I would essentially need a variant call on each individual read, if that makes sense? ...
written 8 months ago by francois10
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Comment: C: How to predict non-sense mediated decay from Illumina reads?
... Yes, I wrote that. I did not get satisfying answers though. Is that an issue you think? Should I delete the stack post? ...
written 8 months ago by francois10
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How to predict non-sense mediated decay from Illumina reads?
... I targetted a protein-coding exon with Cas9, amplified a ~ 150bp product in the region and sequenced with Illumina MiSeq. I now have > 1000X coverage of the region, mapped to my reference genome. Many of these reads have indels, thus potentially inducing a frameshift (if not a multiple of 3). Is ...
sequencing written 8 months ago by francois10
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Why do I have more reads in my .bam file than in my .fastq input file?
... I seem to have more reads after alignment than before. Before alignment ` awk '{s++}END{print s/4}' reads.fastq ` > 153265 After alignment `samtools flagstat align.bam` > 180051 + 0 in total (QC-passed reads + QC-failed reads) > 0 + 0 secondary > 26786 + 0 supplementary > 0 + 0 ...
fastq alignment bam written 17 months ago by francois10 • updated 17 months ago by Pierre Lindenbaum124k

Latest awards to francois

Popular Question 5 months ago, created a question with more than 1,000 views. For With Python, how can I solve this restriction mapping problem?
Popular Question 16 months ago, created a question with more than 1,000 views. For With Python, how can I solve this restriction mapping problem?
Popular Question 17 months ago, created a question with more than 1,000 views. For With Python, how can I solve this restriction mapping problem?
Scholar 17 months ago, created an answer that has been accepted. For A: IGV not highlighting possible variants

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