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3
votes
18
replies
1.4k
views
6 follow
What sequencing/alignment artifact is this?
variants mutect sequencing alignment mitochondria
11 months ago by lacb ▴ 120
1
vote
18
replies
1.3k
views
Find tissues that are functionally related
tissue functionally-related gene-expression
updated 4.0 years ago by 20 • written 4.1 years ago by ▴ 40
20
votes
17
replies
5.5k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein filtering bbmap bbduk phix
6.1 years ago by Anand Rao ▴ 560
3
votes
17
replies
6.6k
views
Removing fastq duplicates
sequence next-gen ChIP-Seq
2.8 years ago by C4 ▴ 10
27
votes
17
replies
19k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
21 months ago by Leite ★ 1.2k
1
vote
17
replies
2.1k
views
Normalizing BLAST results
blast
updated 6.0 years ago by 20 • written 6.1 years ago by • 0
2
votes
17
replies
4.0k
views
Problem With Sam To Bam Converison After Alignment Of Scaffolds To Reference
sam bam alignment samtools
updated 9.7 years ago by 103k • written 9.7 years ago by ★ 1.5k
0
votes
17
replies
2.7k
views
I am not able to let R read my file
R fasta
updated 2.5 years ago by 3.2k • written 2.5 years ago by • 0
0
votes
17
replies
4.4k
views
Finding True SNPs after hard filtering on GATK
SNP
updated 12 months ago by 40k • written 8.0 years ago by ▴ 30
2
votes
17
replies
2.3k
views
Snakemake Megahit error
megahit Snakemake
22 months ago by blackadder ▴ 30
5
votes
17
replies
3.9k
views
Interpreting Genome_Structural_Correction Block_Bootstrap.Py
statistics encode
9.5 years ago by 14134125465346445 ★ 3.6k
1
vote
17
replies
5.3k
views
BBMap: Mapping Fails
BBTools BBMap Mapping
updated 7.5 years ago by 134k • written 7.5 years ago by ▴ 50
4
votes
17
replies
2.4k
views
Any strategy to find out the reason of having unusual Coefficient of Variation (CV) for gene expression data?
microarray gene-expression CV error
4.2 years ago by Jurat Shahidin ▴ 100
0
votes
17
replies
3.3k
views
WGCNA error: "Error in cutreeDynamic"
rna-seq wgcna software error R next-gen
updated 21 months ago by • 0 • written 5.0 years ago by ▴ 20
16
votes
17
replies
2.9k
views
6 follow
RNA seq pipeline
RNA-Seq
5.9 years ago by dimitrischat ▴ 200
12
votes
17
replies
4.2k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python Newick phylogenetics tree phylogeny
5.9 years ago by anonymous1192976466 ▴ 50
7
votes
17
replies
3.9k
views
Strange MA-plot using DESeq2
rna-seq R deseq2
updated 6.7 years ago by 20 • written 6.8 years ago by ▴ 80
8
votes
17
replies
3.6k
views
Getting nan value in vcftool relatedness command?
vcftools relatedness
5.6 years ago by Sharon ▴ 590
0
votes
17
replies
1.2k
views
Transcripts with no read support
RNA-Seq alignment assembly salmon
3.0 years ago by Dunois ★ 2.4k
2
votes
17
replies
7.8k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping genome fastq STAR
updated 18 months ago by • 0 • written 2.7 years ago by • 0
6
votes
17
replies
2.0k
views
6 follow
Issue with reverting bam file back to fastq files
next-gen assembly genome alignment
5.3 years ago by williamsbrian5064 ▴ 480
3
votes
17
replies
2.5k
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing faire mapping
2.5 years ago by boczniak767 ▴ 840
2
votes
17
replies
4.7k
views
Coding Potential Calculator (CPC) error
RNA-Seq
updated 5.5 years ago by 34k • written 5.5 years ago by ▴ 30
0
votes
17
replies
2.4k
views
Fail running blastdb and blastn on my own computer
blast
5.9 years ago by annette440 • 0
7
votes
17
replies
3.4k
views
How to find the differences in aligned bam files
RNA-Seq
6.6 years ago by 1769mkc ★ 1.1k
1
vote
17
replies
3.6k
views
Error executing bedops convert2bed
bedops bed vcf convert2bed
6.7 years ago by lakhujanivijay 5.8k
20
votes
17
replies
2.4k
views
How to add "transcript" feature to a gtf file?
gtf
updated 10 weeks ago by ★ 1.1k • written 2.6 years ago by ▴ 110
4
votes
17
replies
2.4k
views
Cufflinks analysis and gffread
RNA-Seq Assembly
updated 5.9 years ago by 86k • written 5.9 years ago by ▴ 100
3
votes
17
replies
1.2k
views
copy number became inaccurate when downsampling different number fastq reads from a whole fastq file
CNV DownSample fastq copy number not accurate
3.6 years ago by lffu_0032 ▴ 90
9
votes
17
replies
1.9k
views
Creating intergenic bam file
R genome intergenic alignment
7.1 years ago by erincyurtman • 0
7
votes
17
replies
6.2k
views
HeatMap: how to cluster only the rows and keep order of the heatmap's column labels as same as in the df?
R gene genome
5.2 years ago by WUSCHEL ▴ 720
7
votes
16
replies
3.2k
views
How do I get a GFF file
snp
4.2 years ago by apl00028 ▴ 80
0
votes
16
replies
4.2k
views
Issue using MaSuRCA-3.2.6
Assembly assembler
updated 5.1 years ago by 20 • written 5.3 years ago by ▴ 120
3
votes
16
replies
1.1k
views
How to bring all reads to the same length? Any tool?
Read-length Bed
updated 3 months ago by 40k • written 3.7 years ago by ▴ 390
3
votes
16
replies
10k
views
combining z-scores into a single z-score value
excel R statistics
updated 3 months ago by 40k • written 4.5 years ago by ▴ 60
3
votes
16
replies
3.5k
views
GC content of 10x Genomics
fastqc 10x GC content
updated 3.1 years ago by ▴ 170 • written 4.4 years ago by ★ 1.8k
3
votes
16
replies
1.2k
views
Problem, getting information only from the last row and not from all the rows
perl
5.4 years ago by ArusjakGevorgyan ▴ 30
3
votes
16
replies
3.0k
views
FastTree trifurcating Root node
alignment FastTree Phylogenetic Tree
4.7 years ago by Moses ▴ 140
4
votes
16
replies
8.3k
views
STAR - genome indexes generation, genome file not created
RNA-Seq star
updated 4.0 years ago by 20 • written 6.8 years ago by ▴ 70
9
votes
16
replies
1.5k
views
feature extraction from SNPs in R
R gene sequence SNP
4.9 years ago by bioinfo456 ▴ 150
13
votes
16
replies
5.4k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon mask trimming fastq
6.7 years ago by Paul ★ 1.5k
7
votes
16
replies
3.2k
views
cutting overrepresented sequences (recognized by fatsqc)
sequencing genome-sequence fastqc genome sequence
3.5 years ago by Researcher ▴ 20
0
votes
16
replies
3.9k
views
Count read with summarizeOverlaps result 0 for all sample
RNA-Seq
updated 14 months ago by 40k • written 8.4 years ago by ▴ 550
16
votes
16
replies
2.7k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
5.5 years ago by bioinfo456 ▴ 150
5
votes
16
replies
3.8k
views
plotting problem with loop in R
R plot
4.3 years ago by smyiz ▴ 30
9
votes
16
replies
1.1k
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 3.1 years ago by 14k • written 3.1 years ago by ▴ 150
1
vote
16
replies
1.7k
views
Why I see very high mapping percentage, Is this normal or anything wrong in generating libraries?
RNA-Seq hisat2 samtools mapping
updated 5.3 years ago by 20 • written 5.4 years ago by ▴ 730
9
votes
16
replies
3.3k
views
6 follow
covert SAM to full length fasta
fasta SAM
updated 6 months ago by 40k • written 5.1 years ago by ▴ 690
2
votes
16
replies
1.6k
views
I want to know is it a true method ?
vcf SNP realignment
5.5 years ago by Siavash Salek Ardestani ▴ 20
0
votes
16
replies
4.8k
views
Unable To Delete Tmp Files Of Samtools Sort
samtools sort
10.3 years ago by chentong.biology ▴ 50
1,000 results • Page 3 of 20
Recent Votes
C: bowtie2 piped to samtools created many samtools.tmp.bam files, how to get the si
What is the difference between norm --multiallelics -any versus --atomize?
Answer: What is the difference between norm --multiallelics -any versus --atomize?
A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
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Recent Replies
Answer: Importance of Data Structures for Bioinformatics? by xiaoguang ▴ 120
Bioinformatics is a cross-disciplinary research subject and learning anything is a plus for future participation in related jobs. But right…
Answer: How to find positions with higher depth relative to their surroundings by xiaoguang ▴ 120
I saw you want to get regions that have significantly higher depth than their surroundings; you must get a p-value to show significant as w…
Comment: how to calculate BAF and LRR from VCF or BCF files? by xiaoguang ▴ 120
Hi, The ASCAT new version has introduced a new function called `ascat.prepareHTS`, which can be used to prepare all files that are required…
Comment: GERP++ (gerpcol) error on a test data by Diana • 0
I solved the problem in the end. I was under the impression that the reference sequence had to be provided in a separate fasta file: c…
Answer: How to find positions with higher depth relative to their surroundings by d-cameron ★ 2.9k
The usual way of doing this is to use one of the many existing copy number variant caller. Doing this yourself is both a) complicated to do…
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@ _quantum_girl_, as Pierre mentioned, you can annotate your VCF with [snpEff][1] or [ensembl vep][2] once you annotated you could filter n…
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Thank you so much! It is from the same lab but from another project. Would you please explain about combining the counts together a little …
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> how important are Data Structures to multi-omic / bioinformatic analysis Generally speaking, they're not critical if you are using an …
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Update: The above workflow was successful, in that contig_1719 does contain approximately 4 copies of my insert based on searching pieces o…
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I want to find out specific genes using the manhattan plot. I divide the patients into two groups, controls and patients, and try to identi…
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If you don't want to hurt your GPA, why not just take the course pass/fail or, if that's not an option, simply audit it? I doubt anyone wi…
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miRNAs are rather small, and your typical RNASeq library prep will remove small sequences. Are you sure that the data you are trying to ge…
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even these measures will very often not fix the problem in the context of a problem of a problem of perfect separation such as OP describes.
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Hi Amy, I understand, this is why I said, > "The degree to which this is possible depends on the relative content > of each study - e.g. …
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I don't think atomization compares to norm with respect to multiallelic sites. You can see an example of atomatization on a multi-allelic s…
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