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Popular Question to
sunnykevin97
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becko
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english.server
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Recent Replies
Comment: Can IGV simultaneously show alignments for different reference genomes in differ
by
appropiate
▴
40
Thanks @cmdcolin! It looks great, but being relatively new on the field and having started with IGV, I think I will stick to the latter and…
Comment: Extract sequences from a list of ID
by
GenoMax
119k
You need to remove `>` from ID's as the warning tells you to do.
Comment: The best way to get gene lengths for 15K+ genes?
by
manaswwm
▴
260
From my previous experiences in retrieving data in bulk from biomaRt/Ensembl - it is always better to partition your data into batches befo…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ
by
cmdcolin
★
2.3k
disclaimer: I am a jbrowse 2 dev: you could consider jbrowse 2, which can load multiple genomes, visualize synteny, and look at the mapped …
Answer: download just a chromosome from SRA toolkit
by
ATpoint
64k
No, it is not possible since fastq are raw data without alignment information, hence without chromosomal information.
Answer: download just a chromosome from SRA toolkit
by
shelkmike
▴
660
No, its impossible. Sequencing reads in SRA are not partitioned by chromosomes.
Comment: Extract sequences from a list of ID
by
Neel
▴
20
Hi, i want to extract seq from list of id but Seqkit gives this below error and empty output file generated
[WARN] symbol ">" detected…
Answer: Convert mpileup file into dataframe
by
ATpoint
64k
No, don't do any custom data fiddling. Follow the manual of bcftools for variant calling, it covers all you need: https://samtools.github.i…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ
by
GenoMax
119k
You can open multiple instances of IGV and display multiple genome alignments.
Comment: Finding out if a query sequence is present in a read library / bam file (blast a
by
chronotope
▴
10
Thanks for the headsup about the positive control! Any way I can add another pair of reads to the bam file, containing my positive control …
Comment: Order of Normalization/Surrogate variable analysis(or even known batch correctio
by
english.server
▴
280
Thank you for answering my question
Comment: Time Treatment analysis on Rna-Seq
by
ShowPow
▴
20
Hi thanks for the link, I have seen it and there is something I don't understand. For example in 4.8.1 he pass from 147 to 30 (unique) but …
Comment: The best way to get gene lengths for 15K+ genes?
by
JACKY
▴
10
What do you think of this code:
rpkm <- apply(X = subset(counts),
MARGIN = 2,
FUN = function…
Comment: Setting cut-off value
by
ATpoint
64k
What data are this, what kind of analysis are you running, what did you try and where do you get stuck? Did you follow manuals of any tools…
Answer: Order of Normalization/Surrogate variable analysis(or even known batch correctio
by
ATpoint
64k
Typically you would do normalization first, followed by qc. Simply because QC (e.g. PCA) takes as input normalized values so nornalization …
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