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Forum: Questions about going into Bioinformatics from an IT career
career
updated 14 months ago by 43k • written 2.6 years ago by ▴ 10
0
votes
0
replies
508
views
Forum: chimeric vs unaligned reads
alignment star reads chimeric
2.6 years ago by Galileo ▴ 10
0
votes
11
replies
2.3k
views
Forum: Can exons from different reading frames coexist in a peptide sequence?
prediction splicing codons protein exons
updated 2.6 years ago by 14k • written 2.6 years ago by ▴ 100
298
votes
27
replies
45k
views
33 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq sequencing papers
updated 21 months ago by 43k • written 8.3 years ago by ★ 2.4k
0
votes
4
replies
2.1k
views
Forum: Is there really a difference in blastn -task blastn and -task megablast when dealing with unmapped reads?
blastn
2.6 years ago by DNAngel ▴ 250
3
votes
4
replies
1.2k
views
Forum: For what command-line programs or workflows, do you need a graphical user interface for?
GUI
updated 2.6 years ago by ★ 3.2k • written 2.6 years ago by ▴ 320
7
votes
3
replies
1.9k
views
Forum: Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols
fpkm paper tpm
updated 2.6 years ago by 82k • written 2.6 years ago by ▴ 20
0
votes
0
replies
543
views
Forum: Extraction of s-farnesyl cysteine, s-palmitoyl cysteine, disulfide , metal binding
uniprot
updated 17 months ago by 43k • written 2.6 years ago by ▴ 10
37
votes
30
replies
5.1k
views
7 follow
Forum: Spam In Rss Feeds
meta RSS
updated 14 months ago by 43k • written 11.3 years ago by 5.3k
4
votes
8
replies
1.8k
views
Forum: Troubleshooting Tips - bcl2fastq creates duplicate reads
bcl2fastq duplicates readgroup demultiplex
2.7 years ago by DavidStreid ▴ 90
3
votes
1
reply
747
views
Forum: Which bioinformatics tool would you love to see running much faster?
Algorithm optimisation
updated 2.7 years ago by 35k • written 2.7 years ago by • 0
2
votes
2
replies
818
views
Forum: Biostars metadata
Biostars metadata
2.7 years ago by grant.hovhannisyan ★ 2.6k
12
votes
7
replies
7.2k
views
Forum: Differences between SMART-seq2, SMART-seq3, and 10x
cell smartseq UMIs single 10x
updated 7 weeks ago by ★ 6.0k • written 2.7 years ago by ▴ 70
0
votes
2
replies
737
views
Forum: How do I use a small font size in questions and answers?
fonts
updated 2.7 years ago by 100k • written 2.7 years ago by • 0
0
votes
0
replies
533
views
Forum: Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR
RNA-Seq microarray qRT-PCR
2.7 years ago by Antonio R. Franco ★ 5.1k
17
votes
10
replies
6.6k
views
10 follow
Forum: Linearize fasta files
fasta code-golf
updated 2.7 years ago by ▴ 80 • written 5.3 years ago by 16k
1
vote
1
reply
1.0k
views
Forum: What are some of the problems faced by bioinformaticians because the wet lab personell couldn't understand how data analysis was done?
Problems Bioinformaticians wetlab NGS
updated 2.7 years ago by ▴ 590 • written 2.7 years ago by ▴ 10
2
votes
2
replies
947
views
Forum: Internship in research
python genomics
2.7 years ago by vaishnavi ▴ 80
6
votes
2
replies
1.1k
views
Forum: Sequence (annotation) databases in 2021
uniprot annotation sequence ensembl ncbi
updated 2.7 years ago by ★ 2.4k • written 2.7 years ago by ★ 2.5k
17
votes
8
replies
2.8k
views
7 follow
Forum: Where should a biologist start when learning computational biology & systems biology
data-science systems-biology computational-biology
updated 14 months ago by 43k • written 2.7 years ago by ▴ 50
8
votes
11
replies
1.6k
views
6 follow
Forum: Paper: Ten simple rules for biologists initiating a collaboration with computer scientists
article opinion
updated 14 months ago by 43k • written 3.6 years ago by 13k
2
votes
1
reply
736
views
Forum: Advise for a computational neophyte
education research thesis master topic
updated 2.8 years ago by 4.1k • written 2.8 years ago by • 0
26
votes
6
replies
5.6k
views
9 follow
Forum: Making a living with bioinformatics
career
updated 23 months ago by 43k • written 6.0 years ago by ▴ 150
0
votes
3
replies
2.9k
views
Forum: How to calculate LDDT score for protein structure ?
LDDT PBD
updated 2.5 years ago by • 0 • written 2.8 years ago by • 0
13
votes
8
replies
1.9k
views
6 follow
Forum: Why do bioinformatics scientists collaborate and why that's good for science?
Bioinformatics
updated 2.8 years ago by 100k • written 2.8 years ago by ▴ 40
2
votes
3
replies
1.3k
views
Forum: Freelancers for bioinformatics web development
bioinformatics web-development freelance
updated 2.8 years ago by ★ 2.5k • written 2.8 years ago by ▴ 20
0
votes
0
replies
522
views
Forum: Poll about a structured description of a tool, a pipeline
survey pipeline
updated 11 months ago by 43k • written 2.8 years ago by • 0
9
votes
9
replies
1.7k
views
Forum: Opinions on publishing Research as a Blog?
bioinformatics publishing
2.8 years ago by ponganta ▴ 590
6
votes
4
replies
1.1k
views
Forum: What are the major advances in Bioinformatics since 2016
Bioinformatics
updated 14 months ago by 43k • written 2.8 years ago by ▴ 30
1
vote
0
replies
553
views
Forum: Potential applications of the AlfaFold ?
protein-folding
updated 2.8 years ago by 88k • written 2.8 years ago by ▴ 220
9
votes
3
replies
963
views
Forum: How to manage Biostar email subscriptions?
biostars
updated 2.8 years ago by 20 • written 2.8 years ago by ▴ 760
20
votes
12
replies
39k
views
7 follow
Forum: When To Use Sed Awk Over Perl Or Python
perl python awk
updated 14 months ago by 43k • written 10.4 years ago by 9.7k
9
votes
9
replies
3.7k
views
6 follow
Forum: Choose between AMD and INTEL Server CPU in 2021-2022
hardware server
updated 2.9 years ago by 27k • written 2.9 years ago by ▴ 30
2
votes
1
reply
588
views
Forum: Is there a way to look into funding proposals of published papers?
funding
updated 2.9 years ago by ★ 27k • written 2.9 years ago by ▴ 30
5
votes
6
replies
1.3k
views
Forum: Suggestion of Biostatistics book.
RNA-SEQ R Biostatics
updated 2.9 years ago by ★ 2.5k • written 2.9 years ago by ▴ 30
7
votes
2
replies
871
views
Forum: Course on genome assembly and annotation
genomics
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 290
0
votes
1
reply
1.0k
views
Forum: Opinions on SLAM-Seq for Differential Gene Analysis
DGE RNA-Seq htseq
updated 2.9 years ago by ★ 6.0k • written 2.9 years ago by ▴ 70
0
votes
1
reply
590
views
Forum: What can you detect with PE150bp shotgun sequencing with 100X depth
sequencing
updated 2.9 years ago by ★ 2.9k • written 2.9 years ago by ▴ 20
1
vote
4
replies
859
views
Forum: Is WGS reliable for larges indels and duplication?
sequencing
updated 2.9 years ago by ★ 3.4k • written 2.9 years ago by ▴ 20
0
votes
1
reply
1.5k
views
Forum: Basic beginner bioinformatics for biochemistry for university first year students
books course
updated 2.9 years ago by 11k • written 2.9 years ago by • 0
9
votes
7
replies
6.8k
views
6 follow
Forum: When applying to a PhD program in Harvard or MIT, how many publications are recommended?
GradSchool Grad Harvard School Application
updated 2.7 years ago by 43k • written 2.9 years ago by • 0
0
votes
3
replies
722
views
Forum: what for masters?
microbio masters
updated 2.9 years ago by ★ 2.5k • written 3.0 years ago by • 0
0
votes
2
replies
863
views
Forum: Study Materials
learning study materials
2.9 years ago by AHa • 0
6
votes
3
replies
972
views
Forum: Asking for content suggestions for updated bioinformatics book
python
updated 3.0 years ago by 82k • written 3.0 years ago by ▴ 690
9
votes
14
replies
2.5k
views
6 follow
Forum: What are the pain points in genomic variant interpretation/annotation processes?
analysis variant
updated 2.8 years ago by ★ 1.2k • written 3.0 years ago by ▴ 90
4
votes
3
replies
1.5k
views
Forum: Given my background, what are my chances of being accepted into a PhD program at Harvard/MIT?
mit PhD gradschool admission harvard
updated 2.7 years ago by 43k • written 3.0 years ago by • 0
0
votes
2
replies
1.9k
views
Forum: Bioinformatics internship in Europe
europe internship
updated 3.0 years ago by • 0 • written 3.0 years ago by ▴ 70
6
votes
4
replies
1.3k
views
Forum: Detailed Textbooks for bioinformatics and computational biology
biomedical Computational genomics
updated 2.9 years ago by 43k • written 3.0 years ago by ▴ 10
10
votes
7
replies
2.0k
views
Forum: Conceptual - Do I need to justify myself if I generate more than three replicates?
statistics conceptual
3.0 years ago by c_u ▴ 520
2
votes
2
replies
831
views
Forum: reporting differentially expressed genes in a global RNA-seq study
DESeq2 RNA-seq expression heatmaps transcriptomics
3.0 years ago by thomas.welch ▴ 50
1,000 results • Page 5 of 20
Recent Votes
Answer: Genotyping sites with N in reference genome
A: how to combine RNA seq data from 4 lanes
Answer: Cannot install bwa-mem2 via conda
Answer: Sub-sampling a BAM to a fixed number of reads
Comment: Downsample BAM file to specific amount of reads
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
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Scholar to rpolicastro 13k
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Recent Replies
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome by shpak.max ▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Pierre Lindenbaum 161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome by Pierre Lindenbaum 161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline? by yura.grabovska ▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file by asalimih ▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R by Lélé • 0
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations by GenoMax 142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations by Pierre Lindenbaum 161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R by Ghada • 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R by jared.andrews07 ★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
Comment: Duplicated reads (IDs) from nanopore sequencing by GenoMax 142k
If you only have supplementary alignments then they may be caused by reasons mentioned here --> https://www.biostars.org/p/308853/ I did no…
Comment: Cannot install bwa-mem2 via conda by Pierre Lindenbaum 161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Answer: Cannot install bwa-mem2 via conda by Istvan Albert 100k
The problem is caused by running the ARM-based conda. Bioinformatics software is compiled for Intel based CPUs only. Uninstall that versio…
Comment: Duplicated reads (IDs) from nanopore sequencing by marco.barr ▴ 110
[https://www.biostars.org/p/9559284/][1] you could try this [1]: https://www.biostars.org/p/9559284/
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