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Recent Replies
Comment: small RNA-seq length distribution of 100nt?
by
Asaf
10k
How many cycles did you run? Did you measure the RNA length (the actual molecules, not the reads)?
Comment: Constructing single sequence genome assembly out of short reads
by
Asaf
10k
So why not do a reference-guided assembly?
Comment: Difference between proper paired reads and mapped and paired reads
by
Pierre Lindenbaum
162k
sorry, I deleted everything.
Comment: GRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment
by
Maha
•
0
I had the same issue: your fix worked for me too - thanks!
Comment: Constructing single sequence genome assembly out of short reads
by
analyst
▴
50
1. Its bacteria
2. I want to align the reads against assembled genome and compare the results with reference genome alignment
Comment: Difference between proper paired reads and mapped and paired reads
by
QX
•
0
can you share the slide again?
Answer: Exome sequencing dataset
by
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162k
In the burden test, what's interesting is the number of samples case/controls having at least one rare variant in the gene. So one variant…
Comment: Cut&Run replicates handling
by
Asaf
10k
It's essentially bedtools merge of all the replicates. Definitely not replicate aware calling. I'm not sure it's necessary but I don't have…
Comment: Adding CB tag to bam file
by
Maria
•
0
Just for reference, I ended up using
``` java -jar jvarkit.jar samjdk -e 'String c=record.GetReadName(); record.setAttribute("CB",c.substr…
Answer: RNA-seq differentially expressed genes (DEGs) with low fold change values
by
ATpoint
83k
Looks like a typical cell line RNA-seq with a strong biological effect and ver low variability between replicates. What you can do is to te…
Comment: Cut&Run replicates handling
by
ATpoint
83k
It's just an awk merge thing they do, not any replicate-aware calling, no?
Answer: Cut&Run replicates handling
by
Asaf
10k
You can use nf-core [cutandrun][1] pipeline, it supports replicates in the step of consensus peaks calculations.
[1]: https://nf-c…
Comment: Constructing single sequence genome assembly out of short reads
by
Asaf
10k
1. What organism?
2. Why do you want a single genome?
If it's a bacterial genome then most likely contigs will end on rRNA sequences sinc…
Comment: Constructing single sequence genome assembly out of short reads
by
Philipp Bayer
8.5k
Yes Ns are very common in draft genome assemblies.
You'll get them with matepaired reads too: with matepaired data you have 1000 to 5000 …
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