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95,842 results • Page 1 of 1917
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Forum: Will a user #100000 get Tesla Model 3?
milestone
20 minutes ago by Mensur Dlakic ★ 14k
0
votes
2
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78
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Forum: How can I relate bioinformatics to the social behavior of a group of people
behavior Bioinformatics biomedical Social informatics
updated 31 minutes ago by ★ 14k • written 3 hours ago by • 0
2
votes
5
replies
528
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6 follow
Pseudogenes in the human genome annotation
human genome GRCh38 hg38 annotation
updated 3 hours ago by ▴ 540 • written 11 months ago by ▴ 180
0
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0
replies
19
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Adjust for confounding variables with ANCOM-BC
ANCOMBC sequencing microbiome
3 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
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30
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450k Illumina error for some probe converting hg19 to hg38
Illumina450k liftOver
updated 4 hours ago by 34k • written 4 hours ago by ▴ 10
0
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8
replies
158
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Rsubread FeatureCounts return 0.0% assigned
rsubread featurecounts bam rna-seq r
updated 47 minutes ago by 11k • written 4 hours ago by ▴ 10
0
votes
2
replies
152
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Reconstruct SNP haplotypes from Illumina short reads
SNP haplotype
updated 4 hours ago by 139k • written 10 hours ago by • 0
0
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2
replies
69
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Restrict blastp search to set of specific species
taxid blastp
updated 4 hours ago by 107k • written 5 hours ago by • 0
0
votes
1
reply
49
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Residue-residue contact vs protein-protein interactions
machine protein-protein interaction learning deep
updated 5 hours ago by ★ 14k • written 6 hours ago by • 0
0
votes
3
replies
105
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Output file from samtools index is empty
BAI samtools BAM Index
updated 3 hours ago by 17k • written 6 hours ago by • 0
0
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1
reply
77
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Count number of unique alignments to each chromosome from sam file
samtools sort unix uniq sam
updated 4 hours ago by 107k • written 6 hours ago by ▴ 30
8
votes
11
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1.8k
views
Error in fetching the Refseq using Taxonomic ID
eutility NCBI Reference sequence
updated 2 hours ago by • 0 • written 4.2 years ago by ▴ 80
2
votes
3
replies
166
views
How to import a BED file to ChIPseeker in order to visualize genome coverage plot?
ChIPseeker GRanges import ATAC-seq DiffBind
updated 5 hours ago by ★ 1.5k • written 8 hours ago by ▴ 60
0
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0
replies
41
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3' enrichment vs full-length sequencing
RNA sequencing
7 hours ago by vevvo • 0
0
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0
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31
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How to compare two Seurat object (sample) in order to find top markers?
scRNA-SEQ NGS rna-seq
8 hours ago by ahmad mousavi ▴ 550
7
votes
6
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216
views
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
8 hours ago by Istvan Albert 89k
0
votes
2
replies
97
views
Regular Expression for conversion
Linux grep
9 hours ago by shabbas12 • 0
0
votes
3
replies
116
views
how to convert output of bash script to .csv ?
bash csv
updated 4 hours ago by 17k • written 9 hours ago by ▴ 20
0
votes
2
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94
views
paired reads have different names BWA MEM after samtools bam > fastq
alignment
9 hours ago by robert.murphy ▴ 60
2
votes
1
reply
63
views
mapping long-reads to a reference library
bwa TE repeat pacbio
updated 9 hours ago by 54k • written 10 hours ago by ▴ 30
0
votes
3
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324
views
4C-seq data analysis website
genome sequencing software error
updated 10 hours ago by • 0 • written 16 months ago by • 0
1
vote
0
replies
39
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Selection analysis based on each leaves as foreground with FastCodeML
FastCodeML phylogenetictree
10 hours ago by Phela ▴ 10
0
votes
2
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92
views
Extract sequences from a fasta file with specific nucleotide repetition
linux command
updated 11 hours ago by 49k • written 13 hours ago by • 0
0
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0
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32
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Truncated/duplicated genes in Metagenome Assembled Genomes (MAGs) from ONT+Illumina hybrid assembly
hybrid annotation metagenome assembly
12 hours ago by andres.firrincieli ★ 1.8k
1
vote
4
replies
1.6k
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 13 hours ago by 6.0k • written 16 days ago by • 0
0
votes
5
replies
237
views
Diamond blastx: does it support SLURM?
hpc diamond sbatch slurm
updated 11 hours ago by ★ 3.2k • written 21 hours ago by ▴ 30
0
votes
2
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64
views
GATK multiple files run error /usr/bin/bash: gatk: command not found
GATK .bashrc
updated 14 hours ago by 17k • written 15 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
15 hours ago by minuate126 • 0
2
votes
3
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121
views
Queries on 10x sequencing 3' Read 1
10x
updated 10 hours ago by 54k • written 17 hours ago by • 0
3
votes
5
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129
views
How do I compare reads between two bam file?
samtools reads bam compare
updated 14 hours ago by 139k • written 16 hours ago by ★ 1.6k
1
vote
1
reply
72
views
Applying Machine Learning on vcf file
machine vcf learning
updated 15 hours ago by 139k • written 17 hours ago by ▴ 320
0
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2
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139
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Needleman and Wunsch Algorithm
bioinformatics
updated 15 hours ago by 49k • written 20 hours ago by ▴ 90
0
votes
4
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621
views
convert TCGA hg38 maf to hg 19 maf
TCGA liftover maf mutation
updated 20 hours ago by ▴ 40 • written 11 months ago by ▴ 10
0
votes
0
replies
83
views
Two questions about correlation calculation and plotting in R
correlation rstudio spearman pheatmap
20 hours ago by Camilo Andres • 0
0
votes
1
reply
111
views
Looking to start a nanopore sequencing related project
project advice nanopore sequencing
updated 15 hours ago by 17k • written 22 hours ago by • 0
0
votes
0
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72
views
How to extract beta coefficients from edgeR output
rnaseq beta coefficient r edger
updated 13 hours ago by 10k • written 23 hours ago by ▴ 160
1
vote
1
reply
123
views
Looking for volunteer positions
python
updated 1 day ago by ▴ 10 • written 1 day ago by • 0
0
votes
0
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62
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
68
views
Paired end reads not properly aligning in Rsubread align
R pairedend RNAseq
1 day ago by Bonita ▴ 10
0
votes
0
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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
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0
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36
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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
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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
11 hours ago by ziyan • 0
6
votes
7
replies
251
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wc -l or wc -c which linux command is best to find total read count in fastq file?
wc commands
updated 16 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
0
votes
0
replies
32
views
chromoMap Error: .rowNamesDF<-`(x, value = value) : invalid 'row.names' length
chromoMap R
1 day ago by kamanovae ▴ 50
95,842 results • Page 1 of 1917
Recent Votes
C: Coverage plot of a complete genome
A: How to determine alternative splicing read counts
A: How to check the bam file of read quality with graphically visual?
A: How to check the bam file of read quality with graphically visual?
A: Checking bam quality
A: Checking bam quality
C: Error when using ChIPQC package
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Recent Replies
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…
Answer: Pseudogenes in the human genome annotation by Luis Nassar ▴ 540
Hello, You can also use the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) to extract the pseudogenes from our default gene tra…
Comment: Rsubread FeatureCounts return 0.0% assigned by Bonita ▴ 10
OK I will have a look at that. Subread does not index the BAM files so I'll have to do that first.
Comment: Rsubread FeatureCounts return 0.0% assigned by GenoMax 107k
I see it now. Thanks for pointing that out. I suggest that you fire up a genome browser (IGV works well) and examine your alignment files…
Comment: Rsubread FeatureCounts return 0.0% assigned by Bonita ▴ 10
https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/ If you follow the above link there is a button on the right hand side that says Do…
Comment: Rsubread FeatureCounts return 0.0% assigned by GenoMax 107k
Can you post a link for the file? I only see GFF files on the [genome page][1]. [1]: https://www.ncbi.nlm.nih.gov/genome/?term=txid1009…
Comment: Output file from samtools index is empty by cpad0112 17k
can you please run `samtools quickcheck` on your bam file? Here is the manual: https://www.htslib.org/doc/samtools-quickcheck.html and if y…
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