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12 results • Page
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9
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Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
23 hours ago by
vytarasov
▴ 180
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 41 minutes ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
6
votes
6
replies
193
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
updated 9 hours ago by
Mathew
▴ 90 • written 15 hours ago by
sansan_96
▴ 90
2
votes
7
replies
66
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
7 minutes ago by
Matteo Ungaro
▴ 100
2
votes
2
replies
139
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
updated 16 hours ago by
Mathew
▴ 90 • written 18 hours ago by
Azra
▴ 10
1
vote
3
replies
339
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 3 hours ago by
ATpoint
82k • written 8 days ago by
M.
▴ 30
0
votes
0
replies
39
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
6 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
141
views
input file in rmats
rmats
updated 7 hours ago by
Mathew
▴ 90 • written 2 days ago by
Lambodarswain316
• 0
0
votes
1
reply
155
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 15 hours ago by
Mathew
▴ 90 • written 1 day ago by
Christopher
• 0
0
votes
0
replies
5
views
Output file of satools flagstat empty
samtools-flagstat
10 minutes ago by
ramendra.sarma
• 0
0
votes
4
replies
248
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
17 hours ago by
ajbarrett98
• 0
0
votes
2
replies
165
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
1 hour ago by
beginner123
• 0
12 results • Page
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Recent Votes
Answer: joint callset and vcf sorting, unknown TAG issue
Answer: joint callset and vcf sorting, unknown TAG issue
A: what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
A: what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
Gff To Vcf
Comment: Longest transcript variant per gene
Comment: Longest transcript variant per gene
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Pierre Lindenbaum
161k
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Recent Replies
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum I see. I looked up and, although present, the TAG goes like this in both files: `##INFO=<ID=1000gALT,Number=1,Type=Strin…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum much appreciated, thanks for the explanation and possible approaches to solve this. I'm not in the position to run `U…
Comment: Tophat multiple or unique mapping criteria
by
Ruqaiya
• 0
> The --b2-mp defines the mismatch penalty: the first number is used when the quality of the base is good, the second when it's bad. If you…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
> Still, I can't understand the Invalid tag name: "1000gALT" the following line is missing in the VCF header: ##INFO=<ID=1000gALT,Num…
Answer: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
INFO at 121387974 is .;CpG this is an invalid INFO column. There is an invalid attribute named '.' followed by the attribute CpG, …
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum as I don't know the meaning of `.;` and I've seen there are many in both files, I simply removed them with `grep -v`. …
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
My bad I switched positions between the two files when looking the first time. They do indeed look abnormal but how can I fix it? Below the…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py
by
beginner123
• 0
Hi, no I'm using the python implementation as linked above.
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
Show us the content of the INFO column at the problematic positions.
Comment: Tissue-specific DEG analysis with DEseq2
by
ATpoint
82k
Sounds like full confounding. Be careful. Personally I would not do this comparison. There is no way to distinguish tissue effect from dono…
Answer: input file in rmats
by
Mathew
▴ 90
Hi, In the example they give in their GitHub (https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/README.md): They have 2 sample groups wi…
Comment: Longest transcript variant per gene
by
Mathew
▴ 90
I'm glad it worked well for you! Good luck with the rest of your project. I wish you the best.
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thanks so much
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Hello again, It works very well, thank you very much for this solution.
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Hello Mathew, Thanks for your answer, I'll try it and come back.
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