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1,000 results • Page 2 of 20
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7
votes
9
replies
873
views
Tools to check the length of isoforms in reference transcript
transcript histogram isoform
7 months ago by Jjbox ▴ 40
7
votes
8
replies
1.7k
views
How can we time a recent gene duplication event using (neutral?) DNA mutations as molecular clock?
molecular-clock gene-duplication phylogeny
updated 4 months ago by 39k • written 8.1 years ago by ▴ 20
7
votes
8
replies
2.4k
views
Discrepency between number of reads tophat
RNA-Seq tophat software-error
updated 8 months ago by 39k • written 7.8 years ago by ▴ 380
7
votes
12
replies
881
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA integrated ATAC-seq
updated 12 days ago by ▴ 180 • written 18 days ago by ▴ 100
7
votes
7
replies
1.6k
views
LRT test with DESeq2 and how to interpret the results
significant LRT DESeq2 genes RNA-Seq
updated 10 months ago by ★ 1.1k • written 13 months ago by ▴ 20
7
votes
7
replies
825
views
Nextflow rnaseq finishing early
RNA-seq nextflow
updated 10 weeks ago by 39k • written 10 weeks ago by ★ 1.4k
7
votes
4
replies
4.0k
views
IGV genome browser problems
igv
updated 6 months ago by 39k • written 7.9 years ago by ▴ 210
7
votes
6
replies
1.5k
views
How to get/calculate coverage of a gene using bed file?
bed coverage gene
updated 10 weeks ago by 39k • written 19 months ago by ▴ 10
7
votes
16
replies
2.1k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq sequencing
updated 10 weeks ago by 39k • written 5.7 years ago by ★ 3.6k
7
votes
3
replies
767
views
Using a Docker image with ensembl-vep
Linux ensembl-vep Docker
updated 5 months ago by ★ 1.6k • written 5 months ago by ▴ 30
7
votes
10
replies
1.3k
views
Ubuntu 20.04 Crash
Ubuntu
updated 3 months ago by 39k • written 16 months ago by • 0
7
votes
8
replies
3.4k
views
remove duplicated entries from BLAST result file
blast alignment
updated 5 months ago by 39k • written 8.0 years ago by ▴ 170
7
votes
4
replies
1.4k
views
microarray gene datasets
gene
updated 4 months ago by 39k • written 8.1 years ago by ▴ 60
6
votes
3
replies
1.7k
views
PLINK results interpretation
SNP software-error
updated 8 months ago by 39k • written 7.9 years ago by ▴ 40
6
votes
9
replies
962
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM Bowtie
updated 25 days ago by 39k • written 4 months ago by ▴ 40
6
votes
4
replies
2.5k
views
Trouble renaming output files after running PHYLIP programs from a BASH script
PHYLIP sequence software-error
updated 10 months ago by 39k • written 7.5 years ago by ▴ 880
6
votes
6
replies
4.3k
views
Performance of circRNA detection tools
RNA-Seq circRNA
updated 7 months ago by 39k • written 7.8 years ago by ▴ 240
6
votes
13
replies
6.0k
views
DESeq2 and edgeR - no agreement between results
RNA-Seq edgeR DESeq2
updated 10 months ago by 39k • written 7.5 years ago by ▴ 60
6
votes
2
replies
499
views
Need to Modify this
language R
updated 5 months ago by 72k • written 5 months ago by • 0
6
votes
11
replies
927
views
Calculate RPKM
RPKM
11 weeks ago by Chris ▴ 100
6
votes
12
replies
1.3k
views
VCF files 101 - for people from non Bioinformatics Background
vcf sequencing genome variant-calling
updated 12 weeks ago by 39k • written 2.8 years ago by ▴ 20
6
votes
15
replies
1.1k
views
The Best Cloud Solution For Genomics
cloud data-sharing genomics workflow
updated 10 months ago by 39k • written 11 months ago by ▴ 50
6
votes
6
replies
579
views
On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 17 days ago by 72k • written 18 days ago by ▴ 120
6
votes
7
replies
5.9k
views
best alignment tool for Ion Torrent data
chloroplast genome iontorrent
updated 10 months ago by 39k • written 7.5 years ago by ★ 2.3k
6
votes
7
replies
1.4k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters Algorithm Software
updated 24 days ago by 39k • written 6.0 years ago by ▴ 90
6
votes
6
replies
1.2k
views
paired read or not paired read
RNA-Seq
updated 5 months ago by 39k • written 8.1 years ago by ★ 4.2k
6
votes
7
replies
4.5k
views
Creation Of A .Bed File From .Txt
plink
updated 10 weeks ago by 39k • written 9.3 years ago by • 0
6
votes
6
replies
3.2k
views
Bowtie2 classification of discordantly mapped pairs
discordant-pairs bowtie2 alignment
updated 9 months ago by 39k • written 7.7 years ago by ▴ 30
6
votes
2
replies
2.3k
views
Which is the best smoothing technique for replacing zeros from data?
Smoothing
updated 5 months ago by 39k • written 8.0 years ago by ★ 4.2k
6
votes
13
replies
801
views
Error with STAR
STAR
updated 12 weeks ago by 39k • written 3 months ago by ▴ 100
6
votes
7
replies
2.3k
views
Standardizing the language of lab protocols [Current status]
protocols automation
updated 8 months ago by 39k • written 7.7 years ago by ▴ 20
6
votes
7
replies
1.1k
views
The size of the genome in pb of an organism before sequencing?
sequencing genome
updated 10 weeks ago by 39k • written 4.6 years ago by • 0
6
votes
6
replies
4.5k
views
MSD calculations vs time
MDsimulation python computational-biology
updated 6 months ago by 39k • written 7.9 years ago by ▴ 30
6
votes
3
replies
407
views
trimmomatic and STAR alignments
trimmomatic STAR RNAseq sequencing reads
updated 4 weeks ago by ▴ 140 • written 8 weeks ago by ▴ 20
6
votes
4
replies
422
views
Equivalent to SeqMan alignment tool
SeqMan alignments
3 months ago by A_heath ▴ 140
6
votes
9
replies
1.2k
views
for paired-end unmapped reads after star mapping
STAR-mapping Trinity assembly unmapped-reads
updated 9 months ago by 129k • written 9 months ago by • 0
6
votes
6
replies
3.0k
views
What does it mean for a snp to be enriched?
next-gen R SNP genome
updated 10 months ago by 39k • written 7.3 years ago by ▴ 40
6
votes
3
replies
3.2k
views
Comment On The Introduction Of A Bioinformatics Paper
publication bayesian-model
updated 3 months ago by 39k • written 9.2 years ago by ▴ 210
6
votes
5
replies
5.0k
views
MA plots DESeq: strange MA plots
RNA-Seq MAplot DESeq
updated 6 months ago by 39k • written 7.9 years ago by ★ 1.1k
6
votes
7
replies
878
views
to mark the duplicates
Assembly
updated 12 weeks ago by 39k • written 4.0 years ago by ▴ 10
6
votes
12
replies
1.2k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r biomarker
updated 11 weeks ago by 39k • written 4.4 years ago by ▴ 290
6
votes
14
replies
2.7k
views
mapping RNAseq reads to a genbank isoforme that is not in Reference Annotation
RNA-Seq sequence cufflinks new isoform in rnaseq
updated 10 months ago by 39k • written 7.3 years ago by • 0
6
votes
1
reply
2.0k
views
gene expression in bioinformatics
gene-expression
updated 8 months ago by 39k • written 7.8 years ago by • 0
6
votes
9
replies
4.8k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 11 weeks ago by 39k • written 8.2 years ago by ▴ 10
6
votes
2
replies
1.7k
views
Periodicity in SNP calling quality - is this normal?
RNA-Seq VCF GATK SNP
updated 9 months ago by 39k • written 7.7 years ago by 13k
6
votes
6
replies
3.6k
views
Already Working In The Field Of Bioinformatics With A Bachelors, Is A Masters Degree Worth The Time?
masters career
updated 3 months ago by 39k • written 9.7 years ago by ▴ 30
6
votes
12
replies
596
views
Help with error in cellranger
Cellranger
updated 20 days ago by 129k • written 21 days ago by ▴ 100
6
votes
7
replies
4.2k
views
8 follow
desktop bioinformatics platform specs
hardware desktop
updated 5 months ago by 39k • written 8.0 years ago by ▴ 610
6
votes
10
replies
894
views
Understanding bam tracks
RNA sequencing bam
updated 9 months ago by 154k • written 9 months ago by ▴ 30
6
votes
6
replies
962
views
RNA-seq pipeline for degraded RNA
RNA-Seq degraded pipeline alignment
updated 3 months ago by ▴ 80 • written 2.4 years ago by ▴ 60
1,000 results • Page 2 of 20
Recent Votes
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en
Answer: how to choose an efficient filtering threshold to remove shorter and low quality
Contigs to chromosomes annotation
Comment: Contigs to chromosomes annotation
Answer: Contigs to chromosomes annotation
Bioinformatics in drug designing
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Recent Replies
Comment: Limma returned only positive logFC values by LChart 2.6k
It shouldn't, unless there's a misspecification in design. Is it the case that the library sizes are very different between the conditions …
Comment: Contigs to chromosomes annotation by Darked89 4.3k
For a pure contig to Dmel chromosome BLAST should be OK. I am fan of LAST because it is fairly easy to convert MAF to SAM/BAM and then vi…
Comment: Contigs to chromosomes annotation by GenoMax 129k
How many contigs do you have? If the contigs are ~2x number of Drosophila chromosomes (meaning you have long/large contigs) then using a lo…
Comment: Contigs to chromosomes annotation by alexandru.bologa.marian ▴ 50
Thank you for your answer! It would be wrong just to BLAST all the contigs from the draft assembly against each reference chromosome of D.…
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
Several hundred to 10000 DEGs. Would normalization affect logFC?
Answer: Contigs to chromosomes annotation by Darked89 4.3k
Not sure if it is the easiest, but you can map your new assembly to i.e. Dmel genome using LAST: * www: https://gitlab.com/mcfrith/last …
Answer: Gene prediction software by Darked89 4.3k
How complete/polished is your catfish genome assembly? Also: do you have some good quality RNA-Seq? With a draft genome it would be…
Comment: Limma returned only positive logFC values by LChart 2.6k
It'd be helpful to know how many differentially expressed genes there are. If you've got a handful and they're all upregulated, I wouldn't …
Comment: variant allelic fraction by Ram 39k
Cross-posted on bioinfo SE: https://bioinformatics.stackexchange.com/questions/21118/how-to-calculate-the-variant-allelic-fraction-vaf OP,…
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en by GenoMax 129k
You can `cat` the respective R1/R2 files in same order e.g. `cat Run1_R1.fq.gz Run2_R1.fq.gz > R1.fq.gz`.
Comment: too many zeros in 16S rRNA amplicon sequencing data by zhangdengwei ▴ 180
Exactly. I agree that this is due to the NovaSeq which is not very compatible with qimme2 DADA2 pipeline. I finally surrendered to other ap…
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en by ev97 • 0
Thanks for your quick reply! How would you merge them?
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en by Trivas ★ 1.2k
My guess is that some samples were resequenced. I'd recommend just merging the respective R1 and R2s and treat them as one sample.
Comment: Get protein information from ensemblbacteria using interpro by sgiorgetti ▴ 10
@GenoMax Apologies for my belated reply. Agreed, the REST endpoint above supports Ensembl IDs only. Mentioned because both the initial que…
Comment: VEP tab/vcf - Different output by Ben_Ensembl ★ 2.2k
Ah, I see. Then, no, I don't believe that this is possible with the VEP
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