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122,213 results • Page 708 of 2445
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2.2k
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Non-linear relationship between a cell's mitochondrial content and detection of ribosomal genes ssen in single cell rNA seq
RNA-Seq next-gen
updated 4.7 years ago by ▴ 180 • written 4.7 years ago by ▴ 10
1
vote
0
replies
802
views
Forum: Determining Heteroplasmy per sample
heteroplasmy bcftools
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 10
2
votes
3
replies
1.3k
views
Chip-seq balcklisted region information for the latest version of genome ensembl GRCm38
ChIP-Seq alignment
4.7 years ago by luckysardar171 ▴ 20
0
votes
1
reply
924
views
How can I detect small deletion
SNP indel GATAk
4.7 years ago by dyfn1947 • 0
2
votes
4
replies
2.7k
views
HTSeq counts gives zero when I can see the reads in the BAM file
htseq htseq-counts
4.7 years ago by blur ▴ 280
0
votes
1
reply
2.2k
views
Blastn: In The Scoring Parameters, What Does "Linear" Mean?
blastn alignment
updated 4.7 years ago by 20 • written 11.7 years ago by ▴ 180
0
votes
0
replies
1.3k
views
converting bedgraph to Bigwig by HOMER
bedGraph ChIP-seq BigWig HOMER
updated 2.7 years ago by 45k • written 4.7 years ago by • 0
3
votes
4
replies
4.3k
views
GEOquery loading error.
r geo
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by ▴ 10
0
votes
2
replies
1.0k
views
Violation of Independence test for differential methylation (DM)
methylation differential methylation
4.7 years ago by CY ▴ 770
0
votes
3
replies
1.5k
views
GO annotation for zebrafish
RNA-Seq
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
2
votes
2
replies
1.4k
views
Telomere sequence in ncbi human genome assembly?
telomere sequencing dnaseq sequence ttaggg
4.6 years ago by eva_u ▴ 30
0
votes
6
replies
3.2k
views
filtering on F_PASS(GT="het") in bcftools gives contradictory results
SNP filtering bcftools
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 60
2
votes
4
replies
1.6k
views
Single-cell RNAseq for glia
RNA-Seq rna-seq sequencing
updated 4.7 years ago by ★ 1.1k • written 4.7 years ago by • 0
5
votes
5
replies
4.1k
views
nextflow set tuple issue
software error
4.7 years ago by JoeDoasi ▴ 10
1
vote
3
replies
2.4k
views
Facing issue while installing Bio::SeqIO module
bioseqIO
updated 4.7 years ago by 45k • written 4.7 years ago by • 0
1
vote
4
replies
1.1k
views
Whole Genome Sequencing: Identification of genomic differences
genome
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 10
0
votes
0
replies
944
views
FitHiChIP issue input file
next-gen HIChIP
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
3
votes
2
replies
1.3k
views
Data access through python
SNP ExAC ANNOVAR refGene python
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
0
votes
2
replies
1.3k
views
Why I can't download gtf files from GenCode
gene R
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
0
votes
2
replies
2.0k
views
FASTQ,BAM and VCF file size for 300X WES samples
next-gen sequencing storage
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 10
0
votes
0
replies
1.0k
views
Gatk spark beta
gatk genome spark
4.7 years ago by quentin54520 ▴ 120
0
votes
2
replies
1.7k
views
How to align zebrafish RNA-seq data against a reference genome with splice sites using hisat2?
hisat2 zebrafish alignment RNA-Seq fastq
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 30
1
vote
1
reply
1.2k
views
how to determine low quality variants in vcf files
vcf variant_depth
4.7 years ago by pt.taklifi ▴ 70
7
votes
17
replies
6.2k
views
Sciclone on exome sequencing data
sciclone exome seq copy number
updated 4.7 years ago by 20 • written 9.7 years ago by ▴ 160
2
votes
3
replies
6.1k
views
where can I download convertf (to convert vcf/plink files into eigenstrat)
eigenstrat convertf
updated 2.4 years ago by 45k • written 8.1 years ago by ▴ 100
0
votes
0
replies
796
views
Graphtyper vs GATK
Graphtyper GATK
4.7 years ago by Friyunnwoo ▴ 20
0
votes
0
replies
948
views
How to compare two datasets of proteomic analysis when there are unique and common proteins?
proteomics mass spectrometry protein replication
4.7 years ago by Farah ▴ 80
0
votes
3
replies
1.8k
views
top geo ontology
RNA-Seq
4.7 years ago by aranyak111 • 0
2
votes
1
reply
3.2k
views
BOLD systems database for qiime?
qiime BOLD
updated 4.7 years ago by 20 • written 9.0 years ago by ▴ 870
1
vote
2
replies
1.7k
views
plotting the tree in XGBoost
XGBoost
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 80
0
votes
2
replies
1.6k
views
Error occur during tophat2 downloading
tophat2 make
updated 4.7 years ago by 13k • written 4.8 years ago by ▴ 40
0
votes
0
replies
952
views
Cox regression on Splicing. PSI in 0 to 1 or 0 to 100 range
cox RNA-Seq
4.7 years ago by mario.keller1988 • 0
4
votes
4
replies
1.6k
views
How do I remove Batch Effects from Two Separate raw RNA SEQ datasets
RNA-Seq comBat-seq datasets
4.7 years ago by merfer0206 • 0
0
votes
1
reply
2.0k
views
TrimGalore! not properly removing low quality base calls.
RNA-Seq
updated 4.7 years ago by 20 • written 4.8 years ago by • 0
4
votes
4
replies
1.3k
views
Forum: Looking for a CS PhD Program + tips
PhD
updated 2.7 years ago by 45k • written 4.7 years ago by • 0
2
votes
2
replies
3.6k
views
How to deal with the issue when STRING database could not find a protein, or instead matched its similar protein?
proteomics STRING interaction network uniprot
updated 4.7 years ago by ▴ 80 • written 4.7 years ago by ▴ 80
1
vote
1
reply
1.1k
views
How could I change the transparency of the a density plot in ggpairs function (GGally)
R software error
updated 4.7 years ago by ★ 90k • written 4.7 years ago by • 0
29
votes
4
replies
10k
views
Forum: Update to tbb (2021.1.1, conda-forge) breaks bowtie2 (bioconda)
software-error bowtie2 bioconda conda tbb
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 240
1
vote
2
replies
985
views
Gene expression and chromatin state
DNA expression chromatin
4.7 years ago by whb ▴ 60
0
votes
3
replies
1.3k
views
Alignment: how to deal with read mapped on decoy
alignment genome
updated 4.5 years ago by ▴ 60 • written 4.7 years ago by ▴ 120
0
votes
0
replies
1.2k
views
Nanopolish makerange for smaller contigs
assembly genome
4.7 years ago by SUDOsundu ▴ 80
3
votes
3
replies
7.7k
views
VCFTOOLS --recode and --recode-INFO-all
SNP gene vcf
updated 4.7 years ago by 20 • written 7.6 years ago by ▴ 250
0
votes
3
replies
1.2k
views
Query regarding variant calling and reporting
clinical exome whole exome compound heterozygous
4.7 years ago by luffy ▴ 130
0
votes
1
reply
1.2k
views
Biopython byte positions are not compatible with bgzip
htslib biopython bgzip
updated 4.7 years ago by ★ 2.0k • written 4.7 years ago by • 0
3
votes
3
replies
4.3k
views
Error in y - mu : non-numeric argument to binary operator - linear regression loop
bulkRNAseq R linear regression
updated 4.7 years ago by ★ 4.8k • written 4.7 years ago by ▴ 160
2
votes
3
replies
1.9k
views
Medaka tools annotation missing QUAL values
haploid medaka variant-calling nanopore
updated 2.1 years ago by 45k • written 4.8 years ago by ▴ 80
0
votes
0
replies
714
views
Does anyone succeded clustering TCGA data?
RNA-Seq TCGA clustering
updated 4.7 years ago by 20 • written 4.8 years ago by • 0
0
votes
3
replies
2.9k
views
Bowtie2 to map multiple fastq.gz files?
bowtie2 for loop
4.7 years ago by karlitavasco87 • 0
0
votes
4
replies
1.3k
views
Finding gene of interest in data downloaded from SRA
SRA RNA-Seq
updated 4.7 years ago by ★ 3.9k • written 4.7 years ago by • 0
2
votes
5
replies
3.9k
views
In blasp their is %identity? how to find similarity percentage in blastP ??
sequencing
updated 2.5 years ago by 45k • written 7.3 years ago by • 0
122,213 results • Page 708 of 2445
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Recent Replies
Answer: How excactly is the Q30 is calculated? by GenoMax 154k
[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
Comment: best practice for diploid variant calling by Matteo Ungaro ▴ 130
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
Answer: Chip-seq analysis Diffbind by ATpoint 90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read by cmdcolin ★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets by GenoMax 154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
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