User: francois

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francois10
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4 months, 2 weeks ago
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Posts by francois

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Comment: C: Why does samtools calmd change the NM tag when generating the MD tag?
... Yes. Just as a sanity check: Alignment command was ``` minimap2 -ax map-ont hg38.fa \ 110618_pool.fastq.gz > 110618.sam ``` Then samtools `view` / `sort` / `index` And now: ``` samtools calmd 110618s.bam hg38.fa -b > 110618smd.bam ``` ...
written 4 months ago by francois10
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Why does samtools calmd change the NM tag when generating the MD tag?
... I used `samtools calmd` to generate MD tags. While it was running, I noticed it started changing NM tags in my bam file. For example: > [bam_fillmd1] different NM for read > '783b5c4e-8ef2-469f-b278-ead281a35278': 72 -> 1074 While this behaviour seems normal (http://www.htslib.org/doc/sa ...
sequencing written 4 months ago by francois10
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How to report coverage at overlapping regions of paired-end reads?
... I have seen the question briefly discussed in specific contexts, but as it seems like there is no consensus between different tools on this issue I think it would be useful to report here what the best practice is. So I have Illumina MiSeq paired-end reads. Let's say a region is covered by a single ...
illumina paired-end written 10 months ago by francois10 • updated 10 months ago by h.mon31k
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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 17 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 19 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 19 months ago by francois10 • updated 19 months ago by Devon Ryan97k
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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 19 months ago by francois10 • updated 19 months ago by Friederike6.5k
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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 20 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 20 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 20 months ago by francois10

Latest awards to francois

Supporter 4 months ago, voted at least 25 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For With Python, how can I solve this restriction mapping problem?
Popular Question 10 months ago, created a question with more than 1,000 views. For With Python, how can I solve this restriction mapping problem?
Popular Question 10 months ago, created a question with more than 1,000 views. For Why do I have more reads in my .bam file than in my .fastq input file?
Popular Question 13 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?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For With Python, how can I solve this restriction mapping problem?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For With Python, how can I solve this restriction mapping problem?
Scholar 2.4 years ago, created an answer that has been accepted. For A: IGV not highlighting possible variants

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