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1,000 results • Page 6 of 20
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12
votes
14
replies
5.8k
views
bedtools intersect error?
ChIP-Seq bedtools intersect
5.2 years ago by star ▴ 350
0
votes
14
replies
2.1k
views
Error using HTSEq_count
HTSeq python
16 months ago by felipead66 ▴ 120
4
votes
14
replies
12k
views
All the reads aligned using STAR have low mapping quality (0-3). What is happening?
mapping quality STAR BWA alignment
7.8 years ago by kirannbishwa01 ★ 1.6k
0
votes
14
replies
1.9k
views
error relate to R
TWAS SNP R
updated 2.9 years ago by 88k • written 2.9 years ago by ▴ 140
5
votes
14
replies
5.8k
views
SPAdes output with assembling warning
spades assembling iontorrent sequence-reads
5.6 years ago by DanielC ▴ 170
3
votes
14
replies
1.3k
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
0
votes
14
replies
2.0k
views
Corrplot heatmap crunched up and unreadable
Corrplot heatmap
23 months ago by mropri ▴ 150
3
votes
14
replies
6.1k
views
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn mbedtls blast linux blast+
updated 4 months ago by ▴ 40 • written 3.1 years ago by • 0
5
votes
14
replies
2.0k
views
Fastqc genome reads
genome fastqc
updated 2.3 years ago by 82k • written 2.3 years ago by ▴ 60
8
votes
14
replies
2.5k
views
6 follow
kallisto pseudoalignment rate is lower than literature
pseudoalignment kallisto RNA-seq
2.9 years ago by johnsonqinz • 0
1
vote
14
replies
3.6k
views
Cuffmerge error(?) for RNA-seq
RNA-Seq
updated 3.3 years ago by • 0 • written 6.3 years ago by ▴ 10
2
votes
14
replies
1.6k
views
VCF2MAF structural variant file issue.
VCF2MAF
updated 9 months ago by 43k • written 9 months ago by ▴ 10
6
votes
14
replies
4.8k
views
Too many contig after genome assembly with Spades
assembly genome sequence
5.5 years ago by ahmad mousavi ▴ 800
2
votes
14
replies
3.0k
views
Reverse complements in BWA
alignment sequence reads
6.3 years ago by dp ▴ 50
15
votes
14
replies
2.0k
views
how can interpret these biologically weird results?
RNA-Seq
updated 3.3 years ago by 20 • written 6.5 years ago by ▴ 330
1
vote
14
replies
3.2k
views
CWL : file could not be created with exception File not found
cwl gatk
7.8 years ago by skanwal ▴ 50
2
votes
14
replies
1.1k
views
heatmap for HTSeq data in R
RNA-Seq
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 170
1
vote
14
replies
3.8k
views
Picard MarkDuplicates shows error (removing pcr duplicates)
snp alignment sequence
updated 5.5 years ago by 88k • written 5.5 years ago by ▴ 20
4
votes
14
replies
3.6k
views
6 follow
Cutadapt installation - user defined directory
cutadapt Installation
5.8 years ago by davide.chiarugi ▴ 20
15
votes
14
replies
3.2k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq bwa mem bowtie2 alignment
6.3 years ago by John ▴ 270
0
votes
14
replies
792
views
frma normalization
affybatch frma mcp-counter
3 months ago by michelafrancesconi9 ▴ 20
4
votes
14
replies
1.2k
views
remove white space in fastq file
fastq
updated 5 months ago by 142k • written 5 months ago by • 0
1
vote
14
replies
3.4k
views
How to convert Haplotypes file to PLINK format data
R plink
updated 12 months ago by 43k • written 6.0 years ago by ▴ 80
1
vote
14
replies
2.0k
views
Can't Make Sense Of Gene Symbols
gene symbol gene ontology entrez myGene python
5.7 years ago by sinifdosyalari12h ▴ 20
2
votes
14
replies
4.8k
views
differential expression volcano plot
R rna-seq sequencing
4.4 years ago by michelle.piquet ▴ 60
0
votes
14
replies
3.0k
views
NCBI Genome Remapping Service- clinical remap
SNP co-ordinate remapping
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 70
7
votes
14
replies
1.5k
views
How to Blast with multiple species - Phylogenetic Analysis
ChIP-Seq alignment sequence
4.0 years ago by dimitrischat ▴ 210
0
votes
14
replies
2.9k
views
hisat2 alignment showing 0% aligned but sam file is 6GB in size.
hisat2 alignment
updated 2.7 years ago by 100k • written 2.7 years ago by ▴ 10
0
votes
14
replies
2.3k
views
how to identify protein protein interactions
proteomics
7.9 years ago by Learner ▴ 280
5
votes
14
replies
7.2k
views
Duplicate/identical reads in fastq file
sequencing fastq
5.4 years ago by cpad0112 21k
5
votes
14
replies
8.0k
views
Microrna Adapter Trimming
updated 10.5 years ago by ★ 3.0k • written 10.5 years ago by ▴ 150
1
vote
14
replies
2.8k
views
Comparing two variant files
variant comparison
updated 3.0 years ago by ▴ 660 • written 3.0 years ago by ▴ 120
4
votes
14
replies
2.7k
views
Is it possible to annotate single genes by snpeff
snp vcf
updated 10 months ago by 43k • written 6.7 years ago by ▴ 70
0
votes
14
replies
3.1k
views
Creating coverage files containing paired-end fragments of particular sizes
BAM bigwig wig bed paired-end
7.1 years ago by mmmmcandrew ▴ 190
10
votes
14
replies
5.0k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig read-length deeptools ATAC-seq
updated 11 months ago by 43k • written 4.3 years ago by ▴ 50
8
votes
14
replies
6.0k
views
Error in BWA-MEM running in linux
RNA-Seq BWA-MEM alignment
updated 6.0 years ago by 142k • written 6.0 years ago by ▴ 170
0
votes
14
replies
1.6k
views
Fastqc error: Cannot encode phred score
RNA-Seq
3.5 years ago by tanukitries • 0
7
votes
14
replies
4.0k
views
Bowtie2 throws error no. 139
bowtie2 ngs alignment software error sequencing
7.2 years ago by anu014 ▴ 190
2
votes
14
replies
2.5k
views
grep command for fasta header
fasta
2.6 years ago by harry ▴ 30
7
votes
14
replies
6.0k
views
transcriptome index for Kalisto
RNA-Seq
updated 7.3 years ago by 20 • written 7.5 years ago by ★ 1.2k
4
votes
14
replies
2.7k
views
ATAC-Seq High Unaligned Percentage
atac-seq
updated 6.0 years ago by 20 • written 6.1 years ago by • 0
16
votes
14
replies
17k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
5.9 years ago by salamandra ▴ 550
1
vote
14
replies
1.3k
views
Differential expression issue
RNA-Seq
4.2 years ago by sabaghianamir70 ▴ 70
2
votes
14
replies
1.9k
views
Annotating the multi sample vcf file
vcf annotation
17 months ago by Peerzada • 0
1
vote
14
replies
2.0k
views
Counts all read zero after alignment?
alignment rna-seq
updated 23 months ago by 43k • written 2.8 years ago by • 0
5
votes
14
replies
1.7k
views
Interpretation for lowfrevariant
vcf
6.4 years ago by Tania ▴ 180
3
votes
14
replies
1.6k
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
2
votes
14
replies
6.0k
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
6
votes
14
replies
3.3k
views
mapping RNAseq reads to a genbank isoforme that is not in Reference Annotation
RNA-Seq sequence cufflinks new isoform in rnaseq
updated 22 months ago by 43k • written 8.3 years ago by • 0
2
votes
14
replies
1.9k
views
Issue with replicating from a research paper-motifs
sequence RNA FASTA MEME motif
updated 5.0 years ago by 12k • written 5.0 years ago by ▴ 20
1,000 results • Page 6 of 20
Recent Votes
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: How to add Ensembl id to cluster.markers in Seurat
How to add Ensembl id to cluster.markers in Seurat
Comment: Duplicated sequence samtools
Answer: Duplicated sequence samtools
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Recent Replies
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by Bibi • 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot by GenoMax 142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files by Tommaso • 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot by Ghada • 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by ATpoint 82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by Bibi • 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by Pierre Lindenbaum 161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by ajbarrett98 • 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by ATpoint 82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim() by ATpoint 82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED? by Umer ▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis by LauferVA 4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2 by Ezequiel • 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot by marco.barr ▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from by ATpoint 82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
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