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Recent Replies
Comment: Method to fill N gaps with de novo assembly
by
samuel.a.odonnell
▴
330
Agreed. Unless they are the same strain, this should probably be avoided.
Can you just use your new denovo assembly for downstream analysis?
Comment: How can I convert this format of S. tuberosum gene sequence ID - Soltu.DM.10G013
by
Pierre Lindenbaum
145k
where did you get this id ? `Soltu.DM.10G013850.1`
Comment: Method to fill N gaps with de novo assembly
by
pablo
▴
210
I didn't know this tool, I will try. I also used https://github.com/malonge/RagTag
Comment: Method to fill N gaps with de novo assembly
by
Juke34
★
6.9k
maybe by cheating around with cobbler (https://github.com/bcgsc/RAILS)?
Comment: Running synteny of 2 strain.
by
dthorbur
▴
220
To my knowledge there are two types of synteny tools: anchored and alignment based (not official names, just my naming convention).
**Anc…
Comment: Method to fill N gaps with de novo assembly
by
Joe
20k
Is the reference exactly the same species/strain? If they aren't basically identical this is probably not a very good idea if you plan to d…
Comment: How to find unique and common genus by comparing 4 different files containing ge
by
Joe
20k
You have already identified in the post that you can solve this with a loop and some `grep` usage.
Spend time thinking about how you break…
Comment: How to remove Duplicates in Sam file using AWK ?
by
cpad0112
20k
samtools markup with -r option. You don't need to remove duplicates. If you mark duplicates, that is enough for downstream tools. Bamutil h…
Comment: Automatic rename of filenames with bash script
by
cpad0112
20k
can you try this?
#!/bin/bash
for filename in *.fasta; do
[ -f "$filename" ] || continue
mv "$filename" "${file…
Comment: How to remove Duplicates in Sam file using AWK ?
by
sunnykevin97
▴
540
Any suggestions, I'm unable to find any such packages that do the job. Do you have anything in mind ?
Answer: Automatic rename of filenames with bash script
by
fracarb8
▴
760
You can use `rename`. Depending on the version installed one of the commands below should do:
rename "1" "" *.fasta
rename "s/1…
Answer: AGP file ENA submission error
by
Juke34
★
6.9k
There is a description how to well perform an AGP file here: https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/
The message says…
Comment: What LOH means in CANVAS
by
Carambakaracho
★
3.0k
`LOH` = loss of heterozygosity
The reference was heterozygous at the position, the sample is not anymore, so you have an `LOH` event. This…
Comment: Donwloading latest version of Mouse ref genome
by
Trivas
▴
210
You can also `wget` directly from Ensembl and might be easier to implement than having to worry about masking the Y PAR region referenced i…
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