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353 results • Page 2 of 8
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0
votes
4
replies
324
views
WGCNA number of modules issue
networks gene WGCNA correlation
6 days ago by 1215045934 ▴ 80
0
votes
4
replies
1.5k
views
Downloading unique data from refseq
fasta bacteria refseq
updated 4 days ago by 38k • written 6.9 years ago by • 0
1
vote
4
replies
760
views
Method to classify given sample into subtype
Breast-Cancer RNA-Seq TCGA-BRCA TCGA
updated 4 days ago by 38k • written 2.4 years ago by • 0
0
votes
4
replies
985
views
Prokka "not a readable non-empty FASTA file"
fasta prokka
updated 5 days ago by 38k • written 11 months ago by • 0
2
votes
4
replies
583
views
Noob question: I want to use TCGA data to compare survival with mutations, how should I do it?
cancer mutations tcga
updated 5 days ago by 38k • written 9 months ago by ▴ 10
0
votes
4
replies
1.7k
views
CIBERSORT: Errors were encountered in input files, run aborted:
deconvolution cibersort
updated 5 days ago by 38k • written 2.1 years ago by ★ 1.7k
3
votes
4
replies
229
views
Creating sample groups from a combination of genes for survival analysis
Survival
7 hours ago by krushnach80 ★ 1.1k
0
votes
4
replies
907
views
Dealing with non overlapping reads
vsearch usearch sequencing illumina amplicon
updated 1 day ago by 38k • written 20 months ago by • 0
0
votes
4
replies
689
views
How to download the final reads of SRA data from NCBI using fastq-dumb
fastq fasta SRA
updated 4 days ago by 38k • written 21 months ago by ▴ 10
1
vote
3
replies
820
views
smartPCA: problem with .evec file
smartpca
updated 36 minutes ago by 38k • written 19 months ago by ▴ 20
2
votes
3
replies
255
views
mRNA Seq
NGS
updated 5 days ago by 38k • written 7 days ago by ▴ 10
1
vote
3
replies
114
views
Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?
QC cutadapt Illumina trimming 3.4
updated 3 hours ago by 127k • written 6 hours ago by • 0
1
vote
3
replies
5.2k
views
How to convert a .gbff to the .gbk using batch method (to do it computationally for several bacteria)
gbff genome gbk
updated 4 days ago by 38k • written 5.3 years ago by ★ 3.9k
0
votes
3
replies
157
views
A problem about saving Rstudio data matrix
data Rstudio matrix
updated 6 days ago by ▴ 320 • written 6 days ago by ▴ 10
2
votes
3
replies
506
views
BWA generating a sam file without alignment information
sam bwa
updated 19 hours ago by 38k • written 13 months ago by • 0
0
votes
3
replies
427
views
GC @5,20,50 : Fraction of GC content in the bases around the variant position
fasta genome GC-content
updated 20 hours ago by 38k • written 10 months ago by ▴ 10
1
vote
3
replies
283
views
FeatureCounts >edgeR > GO
RNA-SEQ
updated 1 day ago by ★ 1.4k • written 2 days ago by ▴ 80
0
votes
3
replies
972
views
conversion between branch length to SNP numbers
snp raxml figtree
updated 4 days ago by 38k • written 3.5 years ago by • 0
1
vote
3
replies
438
views
Hisat2 Script Help
hisat2 mapping
updated 5 days ago by 38k • written 8 months ago by ▴ 10
1
vote
3
replies
1.8k
views
No. of blast hits uploaded in Blast2GO does not match with the actual number of hits in the diamond output xml file
xml diamond blast2go blastx
updated 4 days ago by 38k • written 5.5 years ago by ▴ 160
0
votes
3
replies
400
views
splitting a bam file by XA tag into multiple lines
bam BWA
updated 21 hours ago by 38k • written 9 months ago by ▴ 50
0
votes
3
replies
224
views
Problem in converting SAM to BAM file by DROP SEQ
SAMtoBAM
updated 1 day ago by 38k • written 2 days ago by • 0
1
vote
3
replies
251
views
How to extract/find the actual names of the gene_IDs if they are not fully presented in gtf.file, and link them to the Count.matrix
featureCounts gtf RNA-Seq
updated 1 day ago by 127k • written 1 day ago by ▴ 80
0
votes
3
replies
371
views
Annovar file to maf file conversion
maf R annovar
updated 21 hours ago by 38k • written 9 months ago by • 0
1
vote
3
replies
3.7k
views
How to sort fastq.gz files efficiently
fastq sort
updated 4 days ago by 38k • written 7.0 years ago by ★ 4.1k
1
vote
3
replies
348
views
DESeq2 code to perform DEG analysis
SEseq2 DEG
updated 5 days ago by 38k • written 23 days ago by • 0
0
votes
3
replies
376
views
Using RSem of Trinity, align_and_estimate_abundance.pl script, all folders for sample/condition is not being created
RSem Quantification Trinity
updated 4 days ago by 38k • written 10 months ago by • 0
3
votes
3
replies
334
views
Retrieving information from FASTA file
NGS FASTA VCF
updated 20 hours ago by 38k • written 12 months ago by ▴ 10
1
vote
3
replies
1.5k
views
Merging individual .bed files?
bed bam samtools bamtobed
updated 4 days ago by 38k • written 4.7 years ago by ▴ 60
1
vote
2
replies
940
views
How to convert multiple .vcf files into single .ped (PLINK compatible files)?
vcf ped PLINK WGS
updated 4 days ago by 38k • written 17 months ago by • 0
0
votes
2
replies
135
views
OrthoFinder problem
Sub OrthoFinder iterative processes Bash
5 hours ago by HERMAN ▴ 10
0
votes
2
replies
603
views
Mapping reads to 5 UTR, 3 UTR and CDS
UTR mapping CDS
updated 4 days ago by 38k • written 18 months ago by • 0
0
votes
2
replies
168
views
mrbayes segmentation fault
mrbayes segmentation fault
1 hour ago by dgrace999 • 0
0
votes
2
replies
232
views
Databases for cell lines
Genomics Genetics
updated 5 days ago by 38k • written 7 days ago by • 0
0
votes
2
replies
145
views
Problem with blasting UNMAPPED RNA-seq paired end reads in Jaculus jaculus
RNAseq jaculus unmapped reads
1 day ago by barbarainb • 0
0
votes
2
replies
522
views
Matching the file names with exposure file in TCGA
FPKM exposure TCGA
updated 34 minutes ago by 38k • written 20 months ago by ▴ 490
3
votes
2
replies
205
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
PAAD KM Plot TCGA
1 hour ago by Manav • 0
0
votes
2
replies
301
views
Post-Imputation QC Problem
Imputation
1 day ago by Jesse • 0
2
votes
2
replies
303
views
bcftools annotate -a
bcftools VCF
updated 4 days ago by 38k • written 20 days ago by ▴ 120
2
votes
2
replies
1.1k
views
How to obtain lineage information from taxid?
euitls taxid2lineage accession2taxid
updated 4 days ago by 38k • written 2.4 years ago by ▴ 30
0
votes
2
replies
401
views
How to remove evidence tags and unnecessary information in the uniprot tab file
UNIPROT
updated 20 hours ago by 38k • written 10 months ago by ▴ 10
0
votes
2
replies
553
views
Tools for SNPs and Indels (RNA seq. Nanopore)
Indel RNA-Seq SNP Nanopore
updated 4 days ago by 38k • written 21 months ago by ▴ 10
1
vote
2
replies
605
views
how to download automatically complete genomes with biopython on ncbi
ncbi biopython
updated 1 day ago by 38k • written 22 months ago by ▴ 20
0
votes
2
replies
178
views
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
vcf.gz UnicodeDecodeError ancIBD
2 days ago by wangjincheng • 0
0
votes
2
replies
309
views
When do the PCR Bottlenecking Coefficient
PCR bam chip-seq
updated 1 day ago by 38k • written 10 weeks ago by • 0
0
votes
2
replies
480
views
Genome Dataset (include nucleotide string)
cancer-genome
updated 4 days ago by 38k • written 22 months ago by • 0
0
votes
2
replies
293
views
bed file question! [extract read numbers from bed file]
BED
updated 1 day ago by 38k • written 4 months ago by ▴ 40
0
votes
2
replies
2.1k
views
Plotting .tab/.bam file
matplotlib tab python bam
updated 4 days ago by 38k • written 3.4 years ago by • 0
0
votes
2
replies
1.3k
views
Intersection of flow cytometry and bioinformatics
flow-cytometry
updated 1 day ago by 38k • written 6.3 years ago by ▴ 30
0
votes
2
replies
640
views
Samtools view error: header include @SQ line missing LN tag.
minimap2
updated 4 days ago by 38k • written 23 months ago by • 0
353 results • Page 2 of 8
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Comment: Can I use abundance from Tximport to compare the expression level of transcript
Comment: getting coding exon information from Ensembl API
C: How to install TMAP
If there is a way to link two gosling html components in two <div>s.
A: Using GATK's HaplotypeCaller or Mutect2 for somatic cancer samples with no norma
Comment: KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
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Comment: Manta and alignment name collision by Pierre Lindenbaum 153k
I wrote https://jvarkit.readthedocs.io/en/latest/SamRemoveDuplicatedNames/ to remove this kind of reads, but I'm not sure it's what you're …
Comment: getting coding exon information from Ensembl API by Nobody ▴ 30
can you delete my account please, because i can't do it by myself. Thank you
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin? by twrl8 • 0
Thank you very much! I will try using the singularity options. Thank you for that aswell. I will keep an eye on the docker hub for newer v…
Comment: Is there a site that takes a list of uniprot IDs/gene IDs as input and create ph by Pierre Lindenbaum 153k
ncbi blast a sequence accession vs the other ? then select the multiple sequence alignment view ?
Comment: Can I use abundance from Tximport to compare the expression level of transcript by aimanbarki ▴ 20
So can I average 6 replicates??
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript by Juke34 7.7k
Don't use `--merge_loci` in your command line this was for AGAT version <1.0.0 (and only few scripts), now this is handled via the config.y…
Comment: getting coding exon information from Ensembl API by Ram 38k
> Because you just answer No we don't. I think you're confusing this professional forum contributed to by volunteers with a customer suppo…
Comment: Can I use abundance from Tximport to compare the expression level of transcript by Ram 38k
Oh, you can just use TPM to do that. Within sample comparison is a completely different (and much easier) game.
Comment: ClusterProfiler enrichKEGG – remove organism name in plots? by Sian • 0
Unfortunately yes, there does seem to be a problem with using the older version - when I came to do more analysis yesterday, the enrichKEGG…
Comment: getting coding exon information from Ensembl API by Nobody ▴ 30
Because you just answer when it's a stupid question or when I ask a lot of questions. This is for asking questions not for being judged by …
Comment: KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset by Manav • 0
Thanks, tried working with the dataset and workflow. It worked.
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript by BioinfoBee • 0
@juke34 Thanks again. I changed the config.yaml *should overlapping loci (at CDS level) be merged in a single locus Only one gene is kept,…
Comment: Can I use abundance from Tximport to compare the expression level of transcript by aimanbarki ▴ 20
Thanks, I am not doing any differential. But, Can we say that 6th transcript is relatively more abundance in our sample than other transcri…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin? by zrm22 ▴ 30
It looks like the ImputePipelinePlugin for the minimap2 run does not use the numThreads Option but rather does the numThreadsOnMachine - 2 …
Comment: Can I use abundance from Tximport to compare the expression level of transcript by aimanbarki ▴ 20
@rob Please, Can you or people from your group answer . As I am using one of your paper as my [reference.][1] [1]: https://f1000rese…
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