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115 results • Page
3 of 3
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83
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Public datasets for genome-wide level mRNA-protein correlation calculation?
mRNA
protein
correlation
4 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
99
views
What is the usual basecalls length and reference mapping length relationship?
genome
alignment
rna-seq
updated 3 days ago by
Carlo Yague
8.6k • written 4 days ago by
anne
• 0
0
votes
4
replies
2.7k
views
MACS2 BAMPE and BEDPE gave dramatically different "mean fragment size"
ChIP-Seq
updated 3 days ago by
axol0tl
• 0 • written 6.4 years ago by
Xinwei Han
• 0
0
votes
1
reply
750
views
Error in genetics vcf file - !! Error (genfile::MalformedInputError): Source "file-path/data_chrxx.vcf.gz" is malformed on line 5145934..
vcf
genetics
updated 3 days ago by
m.medinagomez
• 0 • written 2.3 years ago by
Nance
• 0
0
votes
1
reply
146
views
NCBI gene data
Variants
NCBI
updated 3 days ago by
GenoMax
140k • written 3 days ago by
chandrakala.m
• 0
0
votes
1
reply
140
views
How to perform GO enrichment analysis for assembled sequence ?
GO-enrichment
Gene-Ontology
updated 3 days ago by
Ram
43k • written 3 days ago by
Sony
▴ 10
0
votes
0
replies
104
views
How to calculate weighted transcript length for each gene?
salmon
tximport
rna-seq
updated 3 days ago by
Ram
43k • written 3 days ago by
barrypraveen
▴ 130
0
votes
0
replies
97
views
OSCC Dataset downlod using TCGA biolink
R
OSSC
TCGAbiolink
GDC
updated 3 days ago by
Ram
43k • written 4 days ago by
Biogeek
• 0
0
votes
0
replies
88
views
Multifactor Analysis in DiffBind
DiffBind
ChIPseq
ChIP-seq
3 days ago by
erbrocato
• 0
0
votes
2
replies
200
views
how to run limma for large datasets
R
HPC
biostatistics
statistics
updated 3 days ago by
Ram
43k • written 3 days ago by
Bioinfonext
▴ 460
0
votes
0
replies
105
views
MIENTURNET - miRNA enrichment analysis
miRNA-enrichment
mRNA
RNA
updated 3 days ago by
Ram
43k • written 3 days ago by
PBC
▴ 10
0
votes
0
replies
84
views
Metacoder plot_cladogram long calculation times
Metacoder
updated 3 days ago by
Ram
43k • written 3 days ago by
La52dA97b6
• 0
0
votes
0
replies
109
views
Correlation analysis in single-cell sequencing data
scRNA-seq
correlation
scATAC-seq
3 days ago by
Yingying
• 0
0
votes
0
replies
106
views
t2t Reference gtf file
t2t
3 days ago by
Emre
• 0
0
votes
1
reply
149
views
Autodock tools error - The requested operation requires lifting
Autodock
MGLTools
updated 2 days ago by
zx8754
11k • written 3 days ago by
DOMENICA ALEXANDRA
• 0
115 results • Page
3 of 3
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Synthetic lethality and cancer database
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Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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