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807
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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
507
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
540
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
2.6 years ago by DavidStreid ▴ 90
3
votes
1
reply
746
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
812
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 6 weeks ago by ★ 6.0k • written 2.7 years ago by ▴ 70
0
votes
2
replies
735
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 5.2 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
944
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 3.5 years ago by 13k
2
votes
1
reply
731
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 22 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
521
views
Forum: Poll about a structured description of a tool, a pipeline
survey pipeline
updated 10 months ago by 43k • written 2.8 years ago by • 0
9
votes
9
replies
1.6k
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
552
views
Forum: Potential applications of the AlfaFold ?
protein-folding
updated 2.8 years ago by 87k • written 2.8 years ago by ▴ 220
9
votes
3
replies
960
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 2.8 years ago by 27k • written 2.9 years ago by ▴ 30
2
votes
1
reply
585
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
868
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
1000
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
589
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
852
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
1.4k
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
720
views
Forum: what for masters?
microbio masters
updated 2.9 years ago by ★ 2.5k • written 2.9 years ago by • 0
0
votes
2
replies
859
views
Forum: Study Materials
learning study materials
2.9 years ago by AHa • 0
6
votes
3
replies
969
views
Forum: Asking for content suggestions for updated bioinformatics book
python
updated 2.9 years ago by 82k • written 2.9 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 2.9 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
826
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
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Answer: Server or aws cloud- which one is better for gatk pipeline
Comment: Question about methylation location
Comment: Question about methylation location
Comment: Question about methylation location
How to use minimap2?
Comment: RNA seq analysis
Comment: Filtering Multi-sample VCF file for all except one Genotype
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Recent Replies
Answer: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
I've just displayed clipped bases and this is what it shows. Does this look right? ![enter image description here][1] ![enter imag…
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Hi, I really appreciate you taking the time to reply. I'm still learning with IGV and sorry to sound very inexperienced but how would I che…
Answer: In IGV is this a heterogeneous mutation or false call? by Pierre Lindenbaum 161k
there is a clear shift in the depth just close to this mutation, you should set IGV to display the clipped bases + check if there is a DUP …
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
Using fastp, I found that the adapter sequence for the forward read is corresponding to Trans2_rc in the NexteraPE-PE.fa, while for the re…
Comment: cellranger error message by Max • 0
I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Giulio Genovese ▴ 390
@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Pierre Lindenbaum 161k
I think this is useless, in the gatk doc: > For each variant, the tool will look for the target coordinate, reverse-complement and left-al…
Comment: Too many unpaired forward reads found by Trimmomatic by GenoMax 142k
Ideally you will know which adapters to use but if you don't then programs like `fastp` can auto-detect them. You could also use `bbduk.sh`…
Comment: UMI-Tools knee-method has great influence on the results of white list by i.sudbery 19k
With the `--read2-only` option (which isn't available yet on the bioconda version), this will complain about a lack of `--bc-pattern`. How…
Comment: samtools tview symbols by Ruqaiya • 0
What does the star mean then ?
Comment: RNA seq analysis by prifa ▴ 10
it's raw data **fastq.gz**, so for example I have 4 different samples from different tissue, sample A with 3 replicates, samples B,C and D …
Answer: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> The goal is to remove all the variants which are unique to the KWSBambina sample. using jvarkit vcffilterjdk https://jvarkit.readthedo…
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
The first example used the adapter file NexteraPE-PE.fa, but it generated more than 50% unpaired data...... The content of NexteraPE-PE.fa…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
Ok so I definitely didn't understand at first what my goal was. The goal is to remove all the variants which are unique to the KWSBambina…
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