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1,000 results • Page 5 of 20
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2
votes
15
replies
1.6k
views
from protein to tRNA combinations
RNA-Seq rna-seq
written 3.4 years ago by • 0
5
votes
15
replies
5.4k
views
Annotation with snpEFF
annotation vcf snpeff extractFields
updated 5.8 years ago by 20 • written 5.9 years ago by ▴ 960
6
votes
15
replies
1.6k
views
The Best Cloud Solution For Genomics
cloud data-sharing genomics workflow
updated 21 months ago by 43k • written 22 months ago by ▴ 50
1
vote
15
replies
3.7k
views
Install Lefse in Ubuntu 12
install lefse microbiome
5.9 years ago by goh ▴ 10
0
votes
15
replies
2.2k
views
Chromosome accession numbers correspond to which chromosome?
bam chromosome bed
18 months ago by amy__ ▴ 160
6
votes
15
replies
2.7k
views
Why can't I reproduce the same heat map
ggplots R RNA-Seq
updated 5.7 years ago by 20 • written 5.8 years ago by ▴ 140
7
votes
15
replies
2.2k
views
very low coverage when mappin genomic DNA
mapping coverage DNA genomic
updated 2.7 years ago by 82k • written 2.7 years ago by ★ 1.2k
3
votes
15
replies
2.8k
views
fastq reads with primers and truseq indexed adapter
sequencing next-gen sequence
7.1 years ago by jomo018 ▴ 720
5
votes
15
replies
1.9k
views
Testing uniform distribution of SNPs across chromosome
uniform vcf SNP
5.0 years ago by misterie ▴ 110
0
votes
15
replies
3.7k
views
Identify genes in a tophat aligned bam/sam file
blast alignment rna-seq gene
updated 16 months ago by 43k • written 8.9 years ago by • 0
9
votes
15
replies
1.3k
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
5 months ago by analyst ▴ 30
3
votes
15
replies
5.6k
views
Pairwise sequence alignment with Biojava?
sequence-alignment biojava java
updated 2.2 years ago by 43k • written 9.5 years ago by ▴ 360
2
votes
15
replies
1.5k
views
How to call all the allele in samples
SNP
6.0 years ago by Kritika ▴ 260
1
vote
15
replies
3.7k
views
Can I use PICARD (SortSam) instead of SAMTOOLS (sort) for sorting bam files in RNAseq pipeline where HISAT2 is used for alignment.
RNA-Seq software error sequencing next-gen
6.0 years ago by shuksi1984 ▴ 60
7
votes
15
replies
7.1k
views
6 follow
blastn error - NCBI C++ Exception
assembly blast alignment
updated 2.1 years ago by 15k • written 3.1 years ago by ▴ 980
0
votes
15
replies
2.0k
views
compare two NCBI ftp tables
table NCBI
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 20
2
votes
15
replies
4.2k
views
How to interpret reads mapped to genome from samtools flagstat vs TopHat align_summary.txt ?
RNA-Seq
8.0 years ago by Vasu ▴ 770
8
votes
15
replies
2.0k
views
RNAseq differential expression analysis : no significative FDR but significative GO enrichment
RNA-Seq differential expression
4.5 years ago by guillaume.rbt ★ 1.0k
2
votes
15
replies
4.1k
views
Bowtie2 error :: (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
next-gen SNP alignment
updated 4.1 years ago by ▴ 560 • written 4.1 years ago by ▴ 10
1
vote
15
replies
3.7k
views
Fastx quality filter
next-gen RNA-Seq software error sequencing
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
3
votes
15
replies
2.0k
views
Overlapping regions in a BED file
regions BED Sequence exons annotation
22 months ago by Matej • 0
0
votes
15
replies
3.2k
views
SAMFormatException: Did not inflate expected amount error
WES
updated 2.5 years ago by ▴ 20 • written 2.8 years ago by ▴ 20
0
votes
15
replies
2.4k
views
pathway analysis tools for xenopus
pathways omics xenopus
updated 7.8 years ago by 7.5k • written 7.8 years ago by ▴ 90
1
vote
15
replies
1.5k
views
How to reduce my dataset in order to plot it?
correlation igraph
updated 4.7 years ago by 20 • written 4.9 years ago by ▴ 300
6
votes
15
replies
1.6k
views
Reads partly within an exon
RNA-Seq
6.8 years ago by benjyrolls ▴ 70
1
vote
15
replies
3.3k
views
How to perform multiple alignment using MAFFT?
genome alignment gene sequence
3.0 years ago by anikcropscience ▴ 230
6
votes
15
replies
8.4k
views
Strand specific protocol for bowtie2 alignment
bowtie2 rnaseq alignment RNA-Seq
updated 2.5 years ago by 43k • written 8.5 years ago by ▴ 100
10
votes
15
replies
1.8k
views
Can't find a variant which suppose must have in a vcf file
variant-calling bcftools nf-core
10 months ago by Chris ▴ 260
2
votes
15
replies
2.2k
views
to get each covariate with PC loading in PCA
RNA-seq PCA
5.3 years ago by Grace_G ▴ 20
6
votes
15
replies
3.1k
views
Why GSVA returns a matrix with fewer gene-sets?
microarray GSVA
updated 2.3 years ago by ▴ 70 • written 6.1 years ago by ▴ 280
0
votes
15
replies
3.3k
views
how to make a .bam file from fastQ for RNA-seq ion torrent with BBmap
RNA-Seq
6.6 years ago by genya35 ▴ 40
2
votes
15
replies
4.6k
views
Error when indexing a bcf file
vcf bcf
5.7 years ago by Famf ▴ 30
5
votes
15
replies
2.1k
views
Sample contamination level over 30%
next-gen
6.6 years ago by haiying.kong ▴ 360
5
votes
14
replies
7.1k
views
Duplicate/identical reads in fastq file
sequencing fastq
5.3 years ago by cpad0112 21k
2
votes
14
replies
5.9k
views
Using sam-dump in SRA toolkit to download chr20.bam from NA12878
sratoolkit sam-dump
updated 10 months ago by 43k • written 7.1 years ago by ▴ 10
4
votes
14
replies
1.2k
views
remove white space in fastq file
fastq
updated 4 months ago by 142k • written 4 months ago by • 0
2
votes
14
replies
3.0k
views
Reverse complements in BWA
alignment sequence reads
6.2 years ago by dp ▴ 50
4
votes
14
replies
2.6k
views
ATAC-Seq High Unaligned Percentage
atac-seq
updated 6.0 years ago by 20 • written 6.1 years ago by • 0
0
votes
14
replies
1.9k
views
Corrplot heatmap crunched up and unreadable
Corrplot heatmap
23 months ago by mropri ▴ 150
8
votes
14
replies
2.5k
views
6 follow
kallisto pseudoalignment rate is lower than literature
pseudoalignment kallisto RNA-seq
2.8 years ago by johnsonqinz • 0
3
votes
14
replies
6.0k
views
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn mbedtls blast linux blast+
updated 3 months ago by ▴ 40 • written 3.1 years ago by • 0
0
votes
14
replies
3.0k
views
Creating coverage files containing paired-end fragments of particular sizes
BAM bigwig wig bed paired-end
7.1 years ago by mmmmcandrew ▴ 190
3
votes
14
replies
1.2k
views
How to extract specific region from multiple bam files and merge the outputs into single bam?
bam rna-seq
updated 6 months ago by 142k • written 6 months ago by ▴ 770
1
vote
14
replies
4.2k
views
RNAseq: What is the difference between the units log2 (tpm + 0.001) and log2 (norm_count + 1)
IsoPct units RNAseq
2.9 years ago by muet-10 • 0
8
votes
14
replies
2.4k
views
6 follow
Definition of "=" in comparing two genes
sequencing gene
updated 2.5 years ago by 43k • written 9.8 years ago by • 0
3
votes
14
replies
1.5k
views
How to extract just the reads ID, start position and lenght from the alliigned file?
next-gen sequencing
updated 5.8 years ago by 82k • written 5.8 years ago by • 0
7
votes
14
replies
1.4k
views
How to Blast with multiple species - Phylogenetic Analysis
ChIP-Seq alignment sequence
3.9 years ago by dimitrischat ▴ 210
6
votes
14
replies
2.6k
views
What GTF file should I use in htseq?
hisat htseq polyester RNA-Seq
updated 6.4 years ago by 142k • written 6.4 years ago by ▴ 760
0
votes
14
replies
3.2k
views
DESeq2 output and GO analysis
RNA-Seq GO
4.9 years ago by 2nelly ▴ 310
1
vote
14
replies
3.6k
views
Cuffmerge error(?) for RNA-seq
RNA-Seq
updated 3.2 years ago by • 0 • written 6.3 years ago by ▴ 10
1,000 results • Page 5 of 20
Recent Votes
Comment: When should I NOT apply batch correction for my single-cell RNAseq data?
Comment: Bacterial plasmid analysis
Answer: Problem with data downloaded from Short Reads Archive (SRA)
Answer: Super ehancers
Comment: Bacterial plasmid analysis
Answer: Why employ normalization methods, and how can they be utilized in DEG analysis?
Answer: Why employ normalization methods, and how can they be utilized in DEG analysis?
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Recent Replies
Comment: Extract gRNA sequence using cutadapt by gernophil ▴ 80
This topic is almost 5 years old, but I am facing the same (or at least a very similar) issue. I have ngs files from a CRISPR screen that …
Answer: RNA-seq data for deep learning classification by dsull ★ 5.9k
Honestly speaking, if it's deep learning, it probably doesn't matter that much if you use something like TPMs (probably not raw counts, unl…
Comment: How does gene length effect the number of reads mapped by Chen • 0
Thanks for the detailed answer and I really appreciate it! I still have one question about why the number of reads can be influenced by the…
Comment: Split Fastq Files Into Chunks Of 1M Reads by thomas.heigl.ibk • 0
i tried it. it splits, however, when i compare the first 8 lines of the second split file with the according lines from the original file, …
Comment: DiffBind: no peaks in DBA by Ram 43k
> I've also included the txt version of my .csv file No, you added a screenshot of plain text content, which is counterproductive. You can…
Comment: How to access TCGA samples that were treated with a specific drug? by GenoMax 142k
At the GDC portal you have to turn the "therapeutic agents" toggle under "Clinical Data Analysis" on. ![drug][1] For Breast cancer you c…
Answer: Loss of 'var' using concatenation of AnnData objects by Hugo • 0
Similar question has been asked and answered on [scverse discourse](https://discourse.scverse.org/t/loosing-anndata-var-layer-when-using-sc…
Comment: Bacterial plasmid analysis by Zamin Iqbal ▴ 20
Hi Nicole. 1. The clustering will be quite different between pling and the rep types (because plasmids with one rep type can still be ve…
Comment: Do I need to go back and filter my long-reads? by Ram 43k
Do not delete posts that have received feedback. Engage with the user providing you feedback.
Answer: Download eQTL data of one specific gene for all tissues from GTEx by bk11 ★ 2.4k
Please kindly check your result here. You can click `csv` and download the date in this [link][1]. **OR** If you prefer to use R, there i…
Comment: RNAseq one control two conditions, shared and exclusive genes by matteo.levorato • 0
but why not a single matrix with the 3 different condition and then by lfcShrink function get the DEGs of each condition?
Answer: Super ehancers by jared.andrews07 ★ 16k
Sure, you can run it on them. Stitching tends to happen less frequently since the ATAC peaks are generally less wide than H3K27ac, but it'l…
Answer: What purposes can TPM values be used for? by jared.andrews07 ★ 16k
TPMs cannot be used for intersample comparisons, but they can be used for intrasample comparisons (e.g. comparing relative expression level…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
Thank you so much for the recommendation and the very clear explanation , it's much appreciated. I have already made core-gene phylogenies/…
Comment: What purposes can TPM values be used for? by Adam ▴ 30
Have you run FASTQC and checked the mapping efficiency of WT3? > would running DESeq using TPM values help solve my problem? No, DESeq sh…
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