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114 results • Page
3 of 3
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Views
Votes
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0
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77
views
Creating a custom ontology for peptides
ontology
peptide
1 day ago by
Mathew
• 0
0
votes
1
reply
75
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 8 hours ago by
Pierre Lindenbaum
160k • written 8 hours ago by
ekirsch
• 0
0
votes
0
replies
73
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 14 hours ago by
Ram
43k • written 17 hours ago by
udakshi
• 0
0
votes
0
replies
72
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
20 hours ago by
Broccoli
• 0
0
votes
0
replies
68
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
20 hours ago by
blur
▴ 280
0
votes
1
reply
66
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 12 hours ago by
GenoMax
140k • written 13 hours ago by
David Tachiquín
• 0
0
votes
0
replies
65
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 15 hours ago by
Ram
43k • written 21 hours ago by
M'zelle
• 0
0
votes
0
replies
60
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 15 hours ago by
Ram
43k • written 15 hours ago by
Tolga
▴ 20
0
votes
0
replies
55
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
15 hours ago by
alenew.am
• 0
0
votes
0
replies
31
views
Tissue specific mRNA expression dataset in human and mouse
tissue
specificity
6 hours ago by
Shicheng Guo
★ 9.4k
1
vote
0
replies
26
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
5 hours ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
19
views
Convert to ENTREZGENE
maize
ENTREZGENE
3 hours ago by
sansan_96
▴ 50
0
votes
0
replies
9
views
Variant calling of GBS data for polyploid plant
GBS
variants
polyploid
plant
1 hour ago by
analyst
▴ 10
0
votes
0
replies
7
views
Bowtie2 alignment rate
galaxy
alignment
Bowtie
rate
40 minutes ago by
pavithraashokkumar818
• 0
114 results • Page
3 of 3
Recent Votes
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: 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!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Recent Awards •
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Teacher
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Pierre Lindenbaum
160k
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brian.fristensky
▴ 460
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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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