User: francois

gravatar for francois
francois10
Reputation:
10
Status:
New User
Location:
Last seen:
2 weeks, 4 days ago
Joined:
3 years, 7 months ago
Email:
f*******@kroll.be

Posts by francois

<prev • 40 results • page 1 of 4 • next >
0
votes
0
answers
78
views
0
answers
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 18 days ago by francois10
0
votes
0
answers
78
views
0
answers
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 18 days ago by francois10
3
votes
1
answer
181
views
1
answer
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 6 months ago by francois10 • updated 6 months ago by h.mon30k
0
votes
0
answers
299
views
0
answers
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 13 months ago by francois10
0
votes
1
answer
427
views
1
answers
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 15 months ago by francois10
2
votes
1
answer
427
views
6 follow
1
answer
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 15 months ago by francois10 • updated 15 months ago by Devon Ryan96k
2
votes
2
answers
266
views
2
answers
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 15 months ago by francois10 • updated 15 months ago by Friederike5.9k
0
votes
0
answers
400
views
0
answers
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 16 months ago by francois10
0
votes
0
answers
400
views
0
answers
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 16 months ago by francois10
0
votes
0
answers
400
views
0
answers
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 16 months ago by francois10

Latest awards to francois

Supporter 18 days ago, voted at least 25 times.
Popular Question 4 months ago, created a question with more than 1,000 views. For With Python, how can I solve this restriction mapping problem?
Popular Question 6 months ago, created a question with more than 1,000 views. For With Python, how can I solve this restriction mapping problem?
Popular Question 6 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 9 months ago, created a question with more than 1,000 views. For With Python, how can I solve this restriction mapping problem?
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 2.0 years ago, created a question with more than 1,000 views. For With Python, how can I solve this restriction mapping problem?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For With Python, how can I solve this restriction mapping problem?
Scholar 2.1 years ago, created an answer that has been accepted. For A: IGV not highlighting possible variants

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1306 users visited in the last hour