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16
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7
replies
1.7k
views
Forum: Will a user #100000 get Tesla Model 3?
milestone
updated 23 months ago by 98k • written 23 months ago by ★ 24k
2
votes
8
replies
1.4k
views
Forum: Non biology & computer professional interested in bioinformatics
computer-science machine-learning
updated 7 months ago by 40k • written 23 months ago by • 0
0
votes
0
replies
535
views
Forum: PhD Bioinformatics Remote positions
PhD
updated 15 months ago by 40k • written 23 months ago by ▴ 10
1
vote
0
replies
646
views
Forum: Questions about going into Bioinformatics from an IT career
career
updated 6 months ago by 40k • written 23 months ago by ▴ 10
0
votes
0
replies
420
views
Forum: chimeric vs unaligned reads
alignment star reads chimeric
23 months ago by Galileo ▴ 10
0
votes
11
replies
1.9k
views
Forum: Can exons from different reading frames coexist in a peptide sequence?
prediction splicing codons protein exons
updated 23 months ago by 13k • written 23 months ago by ▴ 90
294
votes
27
replies
43k
views
33 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq sequencing papers
updated 14 months ago by 40k • written 7.7 years ago by ★ 2.4k
0
votes
4
replies
1.7k
views
Forum: Is there really a difference in blastn -task blastn and -task megablast when dealing with unmapped reads?
blastn
23 months ago by DNAngel ▴ 240
3
votes
4
replies
992
views
Forum: For what command-line programs or workflows, do you need a graphical user interface for?
GUI
updated 24 months ago by ★ 3.2k • written 24 months ago by ▴ 310
7
votes
3
replies
1.6k
views
Forum: Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols
fpkm paper tpm
updated 24 months ago by 76k • written 24 months ago by ▴ 20
0
votes
0
replies
450
views
Forum: Extraction of s-farnesyl cysteine, s-palmitoyl cysteine, disulfide , metal binding
uniprot
updated 9 months ago by 40k • written 2.0 years ago by ▴ 10
37
votes
30
replies
4.4k
views
7 follow
Forum: Spam In Rss Feeds
meta RSS
updated 7 months ago by 40k • written 10.7 years ago by 5.3k
4
votes
8
replies
1.5k
views
Forum: Troubleshooting Tips - bcl2fastq creates duplicate reads
bcl2fastq duplicates readgroup demultiplex
2.0 years ago by DavidStreid ▴ 90
3
votes
1
reply
659
views
Forum: Which bioinformatics tool would you love to see running much faster?
Algorithm optimisation
updated 2.0 years ago by 35k • written 2.0 years ago by • 0
2
votes
2
replies
656
views
Forum: Biostars metadata
Biostars metadata
2.0 years ago by grant.hovhannisyan ★ 2.5k
10
votes
3
replies
5.1k
views
Forum: Differences between SMART-seq2, SMART-seq3, and 10x
cell smartseq UMIs single 10x
updated 2.0 years ago by ★ 4.6k • written 2.0 years ago by ▴ 20
0
votes
2
replies
608
views
Forum: How do I use a small font size in questions and answers?
fonts
updated 2.1 years ago by 98k • written 2.1 years ago by • 0
0
votes
0
replies
445
views
Forum: Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR
RNA-Seq microarray qRT-PCR
2.1 years ago by Antonio R. Franco ★ 5.1k
17
votes
10
replies
5.9k
views
10 follow
Forum: Linearize fasta files
fasta code-golf
updated 2.1 years ago by ▴ 80 • written 4.6 years ago by 16k
1
vote
1
reply
898
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 2.1 years ago by ▴ 590 • written 2.1 years ago by ▴ 10
2
votes
2
replies
785
views
Forum: Internship in research
python genomics
2.1 years ago by vaishnavi ▴ 80
6
votes
2
replies
946
views
Forum: Sequence (annotation) databases in 2021
uniprot annotation sequence ensembl ncbi
updated 2.1 years ago by ★ 2.3k • written 2.1 years ago by ★ 2.4k
17
votes
8
replies
2.2k
views
7 follow
Forum: Where should a biologist start when learning computational biology & systems biology
data-science systems-biology computational-biology
updated 6 months ago by 40k • written 2.1 years ago by ▴ 50
8
votes
11
replies
1.3k
views
6 follow
Forum: Paper: Ten simple rules for biologists initiating a collaboration with computer scientists
article opinion
updated 6 months ago by 40k • written 2.9 years ago by 13k
2
votes
1
reply
591
views
Forum: Advise for a computational neophyte
education research thesis master topic
updated 2.1 years ago by 4.1k • written 2.1 years ago by • 0
26
votes
6
replies
5.2k
views
9 follow
Forum: Making a living with bioinformatics
career
updated 15 months ago by 40k • written 5.3 years ago by ▴ 150
0
votes
3
replies
2.4k
views
Forum: How to calculate LDDT score for protein structure ?
LDDT PBD
updated 22 months ago by • 0 • written 2.1 years ago by • 0
13
votes
8
replies
1.5k
views
6 follow
Forum: Why do bioinformatics scientists collaborate and why that's good for science?
Bioinformatics
updated 2.1 years ago by 98k • written 2.1 years ago by ▴ 40
2
votes
3
replies
1.1k
views
Forum: Freelancers for bioinformatics web development
bioinformatics web-development freelance
updated 2.1 years ago by ★ 2.4k • written 2.1 years ago by ▴ 20
0
votes
0
replies
418
views
Forum: Poll about a structured description of a tool, a pipeline
survey pipeline
updated 3 months ago by 40k • written 2.2 years ago by • 0
9
votes
9
replies
1.3k
views
Forum: Opinions on publishing Research as a Blog?
bioinformatics publishing
2.2 years ago by ponganta ▴ 590
6
votes
4
replies
907
views
Forum: What are the major advances in Bioinformatics since 2016
Bioinformatics
updated 6 months ago by 40k • written 2.2 years ago by ▴ 30
1
vote
0
replies
455
views
Forum: Potential applications of the AlfaFold ?
protein-folding
updated 2.2 years ago by 86k • written 2.2 years ago by ▴ 200
9
votes
3
replies
770
views
Forum: How to manage Biostar email subscriptions?
biostars
updated 2.2 years ago by 20 • written 2.2 years ago by ▴ 720
20
votes
12
replies
38k
views
7 follow
Forum: When To Use Sed Awk Over Perl Or Python
perl python awk
updated 6 months ago by 40k • written 9.7 years ago by 9.7k
9
votes
9
replies
3.3k
views
6 follow
Forum: Choose between AMD and INTEL Server CPU in 2021-2022
hardware server
updated 2.2 years ago by 26k • written 2.2 years ago by ▴ 30
2
votes
1
reply
509
views
Forum: Is there a way to look into funding proposals of published papers?
funding
updated 2.2 years ago by ★ 24k • written 2.2 years ago by ▴ 30
5
votes
6
replies
1.1k
views
Forum: Suggestion of Biostatistics book.
RNA-SEQ R Biostatics
updated 2.2 years ago by ★ 2.4k • written 2.2 years ago by ▴ 30
7
votes
2
replies
719
views
Forum: Course on genome assembly and annotation
genomics
updated 2.3 years ago by 40k • written 2.3 years ago by ▴ 270
0
votes
1
reply
821
views
Forum: Opinions on SLAM-Seq for Differential Gene Analysis
DGE RNA-Seq htseq
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by ▴ 70
0
votes
1
reply
471
views
Forum: What can you detect with PE150bp shotgun sequencing with 100X depth
sequencing
updated 2.3 years ago by ★ 2.9k • written 2.3 years ago by ▴ 20
1
vote
4
replies
675
views
Forum: Is WGS reliable for larges indels and duplication?
sequencing
updated 2.3 years ago by ★ 3.4k • written 2.3 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Forum: Basic beginner bioinformatics for biochemistry for university first year students
books course
updated 2.3 years ago by 11k • written 2.3 years ago by • 0
9
votes
7
replies
4.7k
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 2.1 years ago by 40k • written 2.3 years ago by • 0
0
votes
3
replies
588
views
Forum: what for masters?
microbio masters
updated 2.3 years ago by ★ 2.4k • written 2.3 years ago by • 0
0
votes
2
replies
727
views
Forum: Study Materials
learning study materials
2.3 years ago by AHa • 0
6
votes
3
replies
801
views
Forum: Asking for content suggestions for updated bioinformatics book
python
updated 2.3 years ago by 76k • written 2.3 years ago by ▴ 690
9
votes
14
replies
2.0k
views
6 follow
Forum: What are the pain points in genomic variant interpretation/annotation processes?
analysis variant
updated 2.2 years ago by ▴ 980 • written 2.3 years ago by ▴ 90
4
votes
3
replies
1.4k
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 2.1 years ago by 40k • written 2.3 years ago by • 0
0
votes
2
replies
1.6k
views
Forum: Bioinformatics internship in Europe
europe internship
updated 2.3 years ago by • 0 • written 2.3 years ago by ▴ 40
1,000 results • Page 4 of 20
Recent Votes
Answer: Ties in reranked list
Answer: Ties in reranked list
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
Comment: Error in bowtie2
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
Comment: Using STAR aligner to build index of hg38
Answer: How to sort using samtools
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Recent Replies
Comment: Ties in reranked list by Hamza • 0
I had actually accidentally used ranks instead of Entrez gene ids (but switched later to human Ensembl gene ids). However, without your com…
Comment: Hugo_Symbol to Entrez ID by shakyaram079 • 0
Yes sure. These are all gene IDs BZRAP1, C19orf60, TCEB3 and so on.
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Y • 0
I tried the commands you recommended in the bash/command line. When I tried `find "${bam_directory}" -type f -name "*.bam" | xargs samtools…
Comment: Hugo_Symbol to Entrez ID by GenoMax 134k
Can you provide some examples of HUGO ID's you are unable to convert?
Comment: Using STAR aligner to build index of hg38 by GenoMax 134k
GTF file includes gene models/annotation information. You could also use a program like `salmon/kallisto` with just human transcriptome to…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Pierre Lindenbaum 157k
then test each files. find "${bam_directory}" -type f -name "*.bam" | xargs samtools quickcheck file "${reference_gen…
Answer: Ties in reranked list by alserg ▴ 860
The problem here is not the ties, but that your gene IDs in the pathway list (ensemble human genes) does not match the names of the stats v…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Y • 0
I did not use the space between the `-u` flag and the `-o` flag (the blank line) but I did do what you recommended: # Run CuffDiff wit…
Answer: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Pierre Lindenbaum 157k
how about simply trying: ``` cuffdiff -u "${annotation_gtf}" \ -o "${output_directory}" \ -b "${reference_genome}" \ -p "${num_th…
Comment: Using STAR aligner to build index of hg38 by Grace • 0
Yes, I know also need a GTF file. So the GTF file will include RNA information? Thanks for your answer!!
Comment: STAR Intron Motif Script Gives Segmentation fault Error by Y • 0
I will try and figure it out on my own given what you all have mentioned. Thank you for your time.
Comment: Using STAR aligner to build index of hg38 by Amitm ★ 2.2k
Have you gone through the manual [here][1]. In addition to the genome fasta file, you would also need a GTF file (of gene annotations) to b…
Comment: Highly inflated p-values in GWAS by regenie by 4galaxy77 2.8k
You still definitely need to include principle components as covariates, even if your data is from the same ethnicity. Not including those …
Answer: How to create structural variants ground truth for alignment of two long-read ge by Christophe • 0
Hi, D-genies is using minimap2 to align both genomes and minimap2 is chaining local alignments to produce a global one. If the SV are sm…
Comment: Ties in reranked list by Hamza • 0
In this case there are no results in my fgsea object unfortunately
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