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95,843 results • Page 1 of 1917
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1
vote
2
replies
58
views
Server denied on SRA download
ENA fastq SRA
updated 20 minutes ago by 107k • written 2 hours ago by ▴ 10
0
votes
2
replies
49
views
Forum: Will a user #100000 get Tesla Model 3?
milestone
updated 37 minutes ago by 33k • written 4 hours ago by ★ 14k
0
votes
2
replies
130
views
Forum: How can I relate bioinformatics to the social behavior of a group of people
behavior Bioinformatics biomedical Social informatics
updated 4 hours ago by ★ 14k • written 7 hours ago by • 0
2
votes
5
replies
542
views
6 follow
Pseudogenes in the human genome annotation
human genome GRCh38 hg38 annotation
updated 7 hours ago by ▴ 540 • written 11 months ago by ▴ 180
0
votes
0
replies
32
views
Adjust for confounding variables with ANCOM-BC
ANCOMBC sequencing microbiome
7 hours ago by MaxF ▴ 90
621
votes
156
replies
72k
views
92 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook tutorial training News
updated 3 months ago by 270 • written 4.9 years ago by 89k
0
votes
0
replies
41
views
450k Illumina error for some probe converting hg19 to hg38
Illumina450k liftOver
updated 8 hours ago by 34k • written 8 hours ago by ▴ 10
0
votes
8
replies
218
views
Rsubread FeatureCounts return 0.0% assigned
rsubread featurecounts bam rna-seq r
updated 4 hours ago by 11k • written 8 hours ago by ▴ 10
0
votes
2
replies
165
views
Reconstruct SNP haplotypes from Illumina short reads
SNP haplotype
updated 9 hours ago by 139k • written 15 hours ago by • 0
0
votes
2
replies
80
views
Restrict blastp search to set of specific species
taxid blastp
updated 9 hours ago by 107k • written 9 hours ago by • 0
0
votes
1
reply
58
views
Residue-residue contact vs protein-protein interactions
machine protein-protein interaction learning deep
updated 9 hours ago by ★ 14k • written 11 hours ago by • 0
0
votes
3
replies
120
views
Output file from samtools index is empty
BAI samtools BAM Index
updated 8 hours ago by 17k • written 10 hours ago by • 0
0
votes
1
reply
88
views
Count number of unique alignments to each chromosome from sam file
samtools sort unix uniq sam
updated 8 hours ago by 107k • written 10 hours ago by ▴ 30
8
votes
11
replies
1.8k
views
Error in fetching the Refseq using Taxonomic ID
eutility NCBI Reference sequence
updated 7 hours ago by • 0 • written 4.2 years ago by ▴ 80
3
votes
3
replies
179
views
How to import a BED file to ChIPseeker in order to visualize genome coverage plot?
ChIPseeker GRanges import ATAC-seq DiffBind
updated 9 hours ago by ★ 1.5k • written 12 hours ago by ▴ 60
0
votes
0
replies
45
views
3' enrichment vs full-length sequencing
RNA sequencing
12 hours ago by vevvo • 0
0
votes
0
replies
32
views
How to compare two Seurat object (sample) in order to find top markers?
scRNA-SEQ NGS rna-seq
12 hours ago by ahmad mousavi ▴ 550
7
votes
6
replies
220
views
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
12 hours ago by Istvan Albert 89k
0
votes
2
replies
97
views
Regular Expression for conversion
Linux grep
13 hours ago by shabbas12 • 0
0
votes
3
replies
130
views
how to convert output of bash script to .csv ?
bash csv
updated 9 hours ago by 17k • written 14 hours ago by ▴ 20
0
votes
2
replies
95
views
paired reads have different names BWA MEM after samtools bam > fastq
alignment
13 hours ago by robert.murphy ▴ 60
2
votes
1
reply
65
views
mapping long-reads to a reference library
bwa TE repeat pacbio
updated 14 hours ago by 54k • written 14 hours ago by ▴ 30
0
votes
3
replies
326
views
4C-seq data analysis website
genome sequencing software error
updated 14 hours ago by • 0 • written 16 months ago by • 0
1
vote
0
replies
40
views
Selection analysis based on each leaves as foreground with FastCodeML
FastCodeML phylogenetictree
14 hours ago by Phela ▴ 10
0
votes
2
replies
92
views
Extract sequences from a fasta file with specific nucleotide repetition
linux command
updated 16 hours ago by 49k • written 17 hours ago by • 0
0
votes
0
replies
32
views
Truncated/duplicated genes in Metagenome Assembled Genomes (MAGs) from ONT+Illumina hybrid assembly
hybrid annotation metagenome assembly
16 hours ago by andres.firrincieli ★ 1.8k
1
vote
4
replies
1.7k
views
Error: package or namespace load failed for ‘clusterProfiler’: object ‘get_fun_from_pkg’ is not exported by 'namespace:rvcheck'
clusterProfiler namespace offtopic get_fun_from_pkg rvcheck
updated 17 hours ago by 6.0k • written 17 days ago by • 0
0
votes
5
replies
241
views
Diamond blastx: does it support SLURM?
hpc diamond sbatch slurm
updated 15 hours ago by ★ 3.2k • written 1 day ago by ▴ 30
0
votes
2
replies
66
views
GATK multiple files run error /usr/bin/bash: gatk: command not found
GATK .bashrc
updated 18 hours ago by 17k • written 19 hours ago by ▴ 10
0
votes
0
replies
39
views
How can I be sure that raw read counts are well processed from fastq files?
fastq RNAseq raw-count
19 hours ago by minuate126 • 0
2
votes
3
replies
122
views
Queries on 10x sequencing 3' Read 1
10x
updated 14 hours ago by 54k • written 21 hours ago by • 0
3
votes
5
replies
131
views
How do I compare reads between two bam file?
samtools reads bam compare
updated 19 hours ago by 139k • written 20 hours ago by ★ 1.6k
1
vote
1
reply
72
views
Applying Machine Learning on vcf file
machine vcf learning
updated 19 hours ago by 139k • written 21 hours ago by ▴ 320
0
votes
2
replies
140
views
Needleman and Wunsch Algorithm
bioinformatics
updated 20 hours ago by 49k • written 1 day ago by ▴ 90
0
votes
4
replies
622
views
convert TCGA hg38 maf to hg 19 maf
TCGA liftover maf mutation
updated 1 day ago by ▴ 40 • written 11 months ago by ▴ 10
0
votes
0
replies
85
views
Two questions about correlation calculation and plotting in R
correlation rstudio spearman pheatmap
1 day ago by Camilo Andres • 0
0
votes
1
reply
112
views
Looking to start a nanopore sequencing related project
project advice nanopore sequencing
updated 19 hours ago by 17k • written 1 day ago by • 0
0
votes
0
replies
74
views
How to extract beta coefficients from edgeR output
rnaseq beta coefficient r edger
updated 18 hours ago by 10k • written 1 day ago by ▴ 160
1
vote
1
reply
125
views
Looking for volunteer positions
python
updated 1 day ago by ▴ 10 • written 1 day ago by • 0
0
votes
0
replies
66
views
Issues generating the annotated.eff.vcf file : Sanity check his should never happen
Error
1 day ago by cae453 • 0
1
vote
1
reply
69
views
Paired end reads not properly aligning in Rsubread align
R pairedend RNAseq
1 day ago by Bonita ▴ 10
0
votes
0
replies
45
views
Is it ok to use z-scores means for inter-sample comparison?
scRNA_seq RNA-seq
1 day ago by fifty_fifty ▴ 20
0
votes
0
replies
36
views
IDs to use for gene data with BiGG model iEC1356_BL21DE3
E.coli model ESCHER BiGG
1 day ago by avangs • 0
0
votes
0
replies
36
views
How to parse Illumina Bead Array Non-Normalized Output File in R
lumi Illumina Bioconductor R Microarray
1 day ago by Anthony • 0
2
votes
2
replies
100
views
Bam file: replace low quality bases with "N"
quality base bam
1 day ago by Jautis ▴ 330
2
votes
5
replies
217
views
clusterprofiler: id conversion & the problem of package "org.Hs.eg.db"
clusterprofile id conversion
15 hours ago by ziyan • 0
6
votes
7
replies
251
views
wc -l or wc -c which linux command is best to find total read count in fastq file?
wc commands
updated 20 hours ago by 49k • written 1 day ago by • 0
0
votes
3
replies
119
views
Uneven coverage of reads - ChIP-Seq
Coverage ChIP-Seq
updated 1 day ago by 54k • written 1 day ago by • 0
0
votes
2
replies
122
views
Creating column that groups data from another columns
R statistics function data
1 day ago by Bioinfo ▴ 20
0
votes
1
reply
53
views
Confused by MACS2 --scale-to option
macs2 macs ChIP ATAC
updated 1 day ago by 54k • written 1 day ago by ▴ 20
95,843 results • Page 1 of 1917
Recent Votes
Comment: How to import a BED file to ChIPseeker in order to visualize genome coverage plo
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
Comment: Server denied on SRA download
Answer: deseq2.r command not found
Answer: deseq2.r command not found
Answer: deseq2.r command not found
C: Coverage plot of a complete genome
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Recent Replies
Answer: Server denied on SRA download by GenoMax 107k
There have been issues with EBI FTP server today. It has been flaky. With some links it works (albeit slowly) with others you simply get er…
Comment: Will a user #100000 get Tesla Model 3? by Alex Reynolds 33k
If user 100k turns out to be a spammer, I will happily take over the responsibility of driving away the grand prize.
Comment: Will a user #100000 get Tesla Model 3? by Ram 34k
Given the rate of spammer accounts, I daresay most of these 1000 new users are spammers. The site is growing quite well, like you say. Than…
Comment: Server denied on SRA download by Mensur Dlakic ★ 14k
A Matrix glitch? ![enter image description here][1] [1]: https://c.tenor.com/SWboygIShmAAAAAd/whoa-deja-vu-matrix-glitch.gif
Comment: deseq2.r command not found by a_bis ▴ 10
Thank you very much. I was trying to run R through the command line but I will also try running it through Rstudio.
Comment: deseq2.r command not found by a_bis ▴ 10
Thank you very much, that was exactly the problem!
Comment: What is the difference between HISAT2 index "genome.tran" and "genome" by vermack • 0
You will likely need the genome_tran.
Comment: SAM Validation Error with CleanSam (Aligment start must be <= reference seq len by Pierre Lindenbaum 139k
the reference used to map the reads is not the same that the one you're using for gatk.
Comment: SAM Validation Error with CleanSam (Aligment start must be <= reference seq len by shpak.max • 0
Running the bam files through the pipeline with Validation_Strategy=Lenient does generate the desired cleaned/sorted files. However, when I…
Answer: How can I relate bioinformatics to the social behavior of a group of people by Mensur Dlakic ★ 14k
Maybe you would be interested in [**FoldIt**][1], which I think is simultaneously a computer game, an exercise in how to harness a collecti…
Comment: Rsubread FeatureCounts return 0.0% assigned by swbarnes2 11k
Rather than just reassure people that you got matching files, can you just show a couple of lines from your .bam and your .gtf, to confirm …
Comment: bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open by John Marshall 2.5k
If you are getting bcftools 1.8, it's probably because you do not have the `conda-forge` channel added. See [bioconda's channel setup instr…
Comment: Rsubread FeatureCounts return 0.0% assigned by Gordon Smyth ★ 3.4k
Subread will sort and index the BAM files if you specify `sortReadsByCoordinates = TRUE` when running `align()`.
Comment: How can I relate bioinformatics to the social behavior of a group of people by Pierre Lindenbaum 139k
see https://www.biostars.org/p/74374/ ; https://www.biostars.org/p/9829/ ; https://www.biostars.org/p/548/ ; ... ?
Comment: Error in fetching the Refseq using Taxonomic ID by Nelo • 0
opps My mistake not very much familiar with this, but will keep in mind next time Actually i got the same isses like this: " ERROR in fil…
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