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15
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440
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6 follow
Forum: Is there a file format better suited for the era of pangenomics than the .vcf? What are its attributes?
VCF file-format genomics
updated 9 hours ago by 21k • written 15 hours ago by ★ 3.0k
1
vote
13
replies
2.1k
views
Forum: Bioinformatics computer upgrade help
computer
updated 10 hours ago by 39k • written 2.9 years ago by ▴ 50
6
votes
5
replies
783
views
Forum: Russian universities for the study of biomedicine
russian-university
updated 10 hours ago by 39k • written 2.9 years ago by ▴ 30
2
votes
9
replies
1.0k
views
Forum: 'No code' data manipulation tools for bioinformatics
software
updated 11 hours ago by 39k • written 2.9 years ago by • 0
23
votes
12
replies
1.4k
views
6 follow
Forum: Whole-Exome Analysis on a Mainstream Desktop PC
NGS whole-exome
updated 11 hours ago by 39k • written 3.0 years ago by 9.9k
2
votes
9
replies
926
views
Forum: Any good idea for bioinfo final presentation?
R
updated 12 hours ago by 39k • written 3.0 years ago by • 0
5
votes
4
replies
923
views
Forum: Consider CodeOcean or other solutions for runnable Biostars answers?
CodeOcean how-to meta
updated 12 hours ago by 39k • written 3.0 years ago by 21k
0
votes
5
replies
805
views
Forum: Advice for a start in Bioinformatics
R next-gen Python
updated 12 hours ago by 39k • written 3.0 years ago by • 0
23
votes
18
replies
1.0k
views
Forum: Versioning of Blast DB and Reproducible Research
database blast reproducible-research
updated 13 hours ago by 39k • written 3.0 years ago by ▴ 50
0
votes
0
replies
951
views
Forum: ssDNA Aptamer structure prediction
aptamer selex
updated 13 hours ago by 39k • written 3.1 years ago by • 0
0
votes
0
replies
667
views
Forum: Where can I find a one-year fellowship in bioinformatics?
Bioinformatics-Minor Postodoctoral-Fellowship
updated 13 hours ago by 39k • written 3.1 years ago by • 0
22
votes
8
replies
1.3k
views
10 follow
Forum: Is there any online course for bioinformatics right now or in the next two or three months?
online-course mooc
updated 16 hours ago by 39k • written 3.1 years ago by ▴ 50
21
votes
18
replies
1.2k
views
Forum: Is it safe to keep our data in github
github
updated 13 hours ago by 39k • written 3.1 years ago by ▴ 70
3
votes
6
replies
1.7k
views
Forum: Choosing the appropriate test for differential analysis: Limma or Mann-Whitney (with BH correction)? Test for normality
R Shapiro-Wilk Limma Mann-Whitney
updated 13 hours ago by 39k • written 3.1 years ago by ▴ 40
1
vote
7
replies
1.2k
views
Forum: Best online certificates / masters for Bioinformatics
learning certification courses online-training
updated 13 hours ago by 39k • written 3.1 years ago by • 0
34
votes
22
replies
2.2k
views
11 follow
Forum: Have we failed as bioinformatician in this time of COVID-19
Bioinformatician COVID-19
updated 13 hours ago by 39k • written 3.1 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Forum: Alternative of Ingenuity Pathway Analysis - QIAGEN to filter Biomarkers
RNA-Seq
updated 13 hours ago by 39k • written 3.1 years ago by • 0
1
vote
0
replies
463
views
Forum: New to bioinformatics
R Python
updated 13 hours ago by 39k • written 3.1 years ago by ▴ 10
30
votes
16
replies
1.5k
views
9 follow
Forum: Which programming langauge shall I start as a beginner in Bioinformatics
programming-language single-cell
updated 16 hours ago by 39k • written 3.1 years ago by • 0
0
votes
1
reply
2.0k
views
Forum: How's the bioinformatics engineering path? How to become a bioinformatics engineer?
machine-learning Bioinformatics-engineer
updated 13 hours ago by 39k • written 3.1 years ago by ▴ 60
0
votes
2
replies
820
views
Forum: Suffix Arrays: looking for an instructive algorithm of SA construction for teaching
suffix-arrays linear-time teaching algorithm
updated 14 hours ago by 39k • written 3.1 years ago by 52k
0
votes
0
replies
605
views
Forum: make sense out of Whole Exome Sequencing on cancer cell lines
next-gen-sequencing Whole-Exome-Sequencing SNP
updated 14 hours ago by 39k • written 3.1 years ago by ▴ 20
0
votes
2
replies
731
views
Forum: 1st-year grad student, plant biology lab, new to bioinformatics -- where to begin?
microarray plant-biology
updated 16 hours ago by 39k • written 3.1 years ago by • 0
0
votes
0
replies
682
views
Forum: Annotation for WGBS
next-gen
updated 16 hours ago by 39k • written 3.1 years ago by ▴ 70
7
votes
9
replies
782
views
Forum: DEG analysis when not replicates are available
NOISeq RNA-Seq edgeR
updated 16 hours ago by 39k • written 3.1 years ago by ★ 5.1k
5
votes
5
replies
695
views
Forum: What will happen to data analysts after COVID-19 pandemic
COVID
updated 16 hours ago by 39k • written 3.1 years ago by ★ 4.2k
2
votes
6
replies
982
views
Forum: Would love to hear from you re: which bionformatics resources could use an improvement in their interface.
seq database gene prot
updated 18 hours ago by 39k • written 3.2 years ago by • 0
2
votes
4
replies
1.0k
views
Forum: Transitioning from Wet Lab to Computational Biology as a PhD Student/Surgeon
RNA-Seq sequencing
updated 17 hours ago by 39k • written 3.1 years ago by ▴ 10
7
votes
5
replies
711
views
Forum: scRNA rising in popularity, what comes next?
scRNA
updated 18 hours ago by 39k • written 3.2 years ago by ▴ 20
12
votes
12
replies
946
views
7 follow
Forum: Who qualify as a world class bioinformatician as seen in job ads
world-class bioinformatician qualification
updated 18 hours ago by 39k • written 3.2 years ago by • 0
30 results • Page 1 of 1
Recent Votes
Differences between trimming tools: cutadapt, bbduk and sickle
C: How sickle (adaptive trimming tool) work.
How sickle (adaptive trimming tool) work.
Comment: Help with running ATAC using Encode pipeline
Answer: Is there a file format better suited for the era of pangenomics than the .vcf? W
Answer: Is there a file format better suited for the era of pangenomics than the .vcf? W
A: Can EdgeR of DeSeq be used for Single-cell RNA-seq?
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Recent Awards • All
Popular Question to kenneditodd ▴ 10
Popular Question to predeus ★ 1.9k
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Recent Replies
Comment: GISTIC from ASCAT by Hyper_Odin ▴ 280
Also, I would like to add that we cannot use ASCAT output for GISTIC input...since GISTIC expects all the chromosomes in the input file eve…
Comment: GISTIC from ASCAT by Hyper_Odin ▴ 280
Hi, Ram thanks for the help...I figured out the issue. somehow I had duplicate files in the folder which caused the issue.
Answer: multiqc: group samples by population + boxplot ? by Phil Ewels ★ 1.2k
You can't group and make boxplots as you describe, probably your best bet is to use the [highlight tool][1] in the report (especially if yo…
Comment: Problem with GPU guppy_basecaller and SLURM by kenneditodd ▴ 10
Nope - but I just noticed another error message in the guppy log. I've seen some people have the same problem on nanopore community but not…
Comment: Where to get the molecular subtype information of STAD sample in TCGA by younglin113 ▴ 50
Thanks a lot! But still a bit curious why this information is not included in GDC or UCSC xena.
Comment: CellRanger problem by Carlos Eduardo • 0
I'm using cellranger mkref --genome=Viral --fasta=path.fna --genes=path.gtf I have 126G RAM
Comment: How do I run DE for TPM values (not CPM)? by John • 0
Thanks, but it's giving me the error that expression object should be numeric and that there are 2 non-numeric columns (because the first t…
Comment: How do I run DE for TPM values (not CPM)? by LChart 2.7k
you're mixing two packages, edgeR ("dgelist") and limma ("lmFit"). Just put your log(1+TPM) matrix as the first argument to lmFit.
Answer: hisat2-align exited with value 1 by GenoMax 130k
You only need to use the `basename` of the index when you specify it. Try hisat2 -p 4 -x /home/ngs/zebra_fish/zebra_fish -U SRR10480…
Comment: How to deal with SRA file without .SRA by Andy ▴ 50
Thank you Ram! Yes, I did something wrong.
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W by Ram 39k
Exactly. Even when we were trying to leverage hail at my previous job, we ran into troubles constantly with data freezes. IMO academia is n…
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W by Jeremy Leipzig 21k
OK hospitals in particular definitely don't want to regenerate anything as individual new samples are added to the variant store. Even the …
Comment: How to deal with SRA file without .SRA by Ram 39k
PRJNA is the standard NCBI BioProject prefix. There are 19 pairs of FASTQs associated with this one so you're doing something wrong
Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W by Ram 39k
> But you can't live out of your suitcase forever. I'd compare it to a local department store vs Walmart - I think cloud/distributed stora…
Comment: How do I run DE for TPM values (not CPM)? by John • 0
That's what I'm trying to do but again, I'm getting an error on the last line and I'm asking how to fix it.
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