User: tiago211287

gravatar for tiago211287
tiago2112871.2k
Reputation:
1,220
Status:
Trusted
Location:
USA
Last seen:
3 days, 5 hours ago
Joined:
5 years, 11 months ago
Email:
t**********@gmail.com

Posts by tiago211287

<prev • 212 results • page 1 of 22 • next >
0
votes
1
answer
102
views
1
answers
Comment: C: Counting single-cell ATAC fragments at peaks on BED file
... Why can't you just use your bed file with your alignment files (BAMs) by using featureCounts software to count the number of fragments in each peak region? ...
written 26 days ago by tiago2112871.2k
4
votes
0
answers
132
views
0
answers
Comment: C: enhanced volcano plot
... You can use Samtools to figure out the command used by the facility to generate the bam file. Look at the @PG tag might see the genome/annotation file names which might give you a clue of the reference used for alignment. > samtools view -H file.bam You generated a Count matrix and then what? W ...
written 26 days ago by tiago2112871.2k
0
votes
2
answers
1.0k
views
2
answers
Comment: C: how to extract the genomic positions and chromosome number for a list of genes
... You can try to convert your retired IDs using the [ID Conversion tool][1] for GRCh37. Or maybe this [Biostar][2] link can help you to access the GRCh37 using biomaRt. This Ensembl [page][3] contains information about converting between both assemblies. [1]: http://grch37.ensembl.org/Homo_sapien ...
written 17 months ago by tiago2112871.2k
0
votes
2
answers
1.0k
views
2
answers
Comment: C: how to extract the genomic positions and chromosome number for a list of genes
... Can you please share a sample of the remaining id's? ...
written 17 months ago by tiago2112871.2k
0
votes
2
answers
1.0k
views
2
answers
Comment: C: how to extract the genomic positions and chromosome number for a list of genes
... You need a column with your regular gene_id_versions called **ensembl_gene_id_version**. And Another column with the edited **ensembl_gene_id** without versions. created with gsub. my_ids$ensembl_gene_id <- gsub("\\..*","", my_ids$ensembl_gene_id_version) Only then you can merge, using: ...
written 17 months ago by tiago2112871.2k
2
votes
2
answers
1.0k
views
2
answers
Answer: A: how to extract the genomic positions and chromosome number for a list of genes
... The numbers after the dot are the gene version. It might be that you have very old gene versions. You may try to use R to get your information. Removing the Ensembl gene version. Like this: #Get gene names annotation source("http://bioconductor.org/biocLite.R") BiocInstaller::biocLite ...
written 17 months ago by tiago2112871.2k
3
votes
1
answer
522
views
1
answers
Comment: C: Bioinformatics question regarding multilevel pie chart
... Maybe Adobe Illustrator? ...
written 17 months ago by tiago2112871.2k
0
votes
0
answers
101
views
0
answers
Comment: C: Deconvolve bulk expression data into individual immune components.
... Maybe Helpful? https://www.nature.com/articles/s41467-018-08023-x ...
written 17 months ago by tiago2112871.2k
1
vote
3
answers
5.2k
views
3
answers
Comment: C: ATAC-seq DE analysis
... Your link does not work anymore. Could you update it? Thanks! ...
written 21 months ago by tiago2112871.2k
0
votes
1
answer
940
views
1
answers
Comment: C: bam file merge
... In http://www.htslib.org/doc/samtools-1.2.html, it says, > -h is specified the @SQ headers of input files will be merged into > the specified header, otherwise they will be merged into a composite > header created from the input headers. If in the process of merging > @SQ lines for coor ...
written 2.1 years ago by tiago2112871.2k

Latest awards to tiago211287

Great Question 14 days ago, created a question with more than 5,000 views. For Removing Outliers from volcano plot
Commentator 26 days ago, created a comment with at least 3 up-votes. For C: Gviz: How to plot transcripts with grouping given transcript names and a TxDb?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For rMATS error in the instalation test
Popular Question 8 months ago, created a question with more than 1,000 views. For rMATS error in the instalation test
Popular Question 8 months ago, created a question with more than 1,000 views. For ggbio package only works with h19 genome
Popular Question 8 months ago, created a question with more than 1,000 views. For Dataset normalization before gene ontology analysis
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Gviz: How to plot transcripts with grouping given transcript names and a TxDb?
Popular Question 13 months ago, created a question with more than 1,000 views. For rMATS error in the instalation test
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Must know algorithms before attending a bioinformatics interview
Popular Question 17 months ago, created a question with more than 1,000 views. For rMATS error in the instalation test
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Gviz: How to plot transcripts with grouping given transcript names and a TxDb?
Popular Question 20 months ago, created a question with more than 1,000 views. For rMATS error in the instalation test
Popular Question 21 months ago, created a question with more than 1,000 views. For rMATS error in the instalation test
Popular Question 22 months ago, created a question with more than 1,000 views. For rMATS error in the instalation test
Great Question 22 months ago, created a question with more than 5,000 views. For What exactly means the Dispersion Plot DESeq2?
Popular Question 22 months ago, created a question with more than 1,000 views. For rMATS error in the instalation test
Popular Question 2.0 years ago, created a question with more than 1,000 views. For rMATS error in the instalation test
Popular Question 2.0 years ago, created a question with more than 1,000 views. For rMATS error in the instalation test
Popular Question 2.0 years ago, created a question with more than 1,000 views. For rMATS error in the instalation test
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Question about the DESeq2: log2foldchange contradictory
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Question about the DESeq2: log2foldchange contradictory
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Question about the DESeq2: log2foldchange contradictory
Guru 2.2 years ago, received more than 100 upvotes.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Question about the DESeq2: log2foldchange contradictory
Appreciated 2.2 years ago, created a post with more than 5 votes. For C: about editing SAM/BAM files

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1102 users visited in the last hour