User: ddowlin

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ddowlin70
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Posts by ddowlin

<prev • 28 results • page 1 of 3 • next >
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Expression data from cufflinks merged gtf
... Hi all, I have assembled six transcriptomes with hisat2/stringtie. I merged the resulting gtf files into a single merged gtf. For many transcripts in the merged gtf a transcript_id starting with 'MSTRG' was created. My understanding is that the MSTRG ids are assigned to transcripts in the merged ...
bedtools gtf stringtie rna-seq written 6 months ago by ddowlin70
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Comment: C: extract fasta sequence using fasta header with python 3
... Grep/awk. But I want to try with python. ...
written 11 months ago by ddowlin70
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(Closed) extract fasta sequence using fasta header with python 3
... Hi all, I have a list of fasta headers and a corresponding multi fasta file. Using python3 I would like to iterate through my list of ids and extract the matching fasta sequence form my fasta file. I, then, want to write each header and sequence to its own fasta file. What is the best approach us ...
fasta python written 11 months ago by ddowlin70
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Comment: C: hisat2-build indexing produces more than 8 output files
... Thanks--I tried without the --ss and --exon options and it seems to have worked OK. ...
written 18 months ago by ddowlin70
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Comment: C: hisat2-build indexing produces more than 8 output files
... Thanks for the suggestion. Unfortunately pre-made indices aren't available for the species I am interested in. ...
written 18 months ago by ddowlin70
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hisat2-build indexing produces more than 8 output files
... Hi all, I am trying to assemble a primate transcriptome using hisat2/stringtie. First I want to index the genome using hisat2. I used both --ss and --exon to provide information on splice sites and exons. The manual states that 8 files should be produced after indexing 1.ht2 to 8.h2t. However, I ...
indexing hisat2 written 18 months ago by ddowlin70 • updated 10 months ago by gaoyufeng11090
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Answer: A: Populate data frame column X with substring from column Y using R
... Well, I quickly found a solution using `stringr` and `dplyr` [here][1]. library(stringr) library(dplyr) df1 <- df1 %>% mutate(accession = str_extract(gene, "XP_[0-9]+\\.*[0-9]*")) gives: gene accession 1 ...
written 22 months ago by ddowlin70
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Populate data frame column X with substring from column Y using R
... Hi all, I have a data frame in R with a column of gene identifiers (taken from fasta headers). These vary and include both Ensembl style (*e.g.* `ENSP000000001`) and NCBI style (*e.g* `gi|123|ref|XP_000001.1|`) as well as others. I want to extract the accession and version numbers from the NCBI i ...
R written 22 months ago by ddowlin70 • updated 22 months ago by cpad011211k
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Comment: C: Finding Ultraconserved elements between human and zebrafish
... Thanks for the suggestion. I have a follow-up question. Do you know how to download all conserved elements as a single table at once? So far, I can only select specific elements from the browser and download them individually. ...
written 2.7 years ago by ddowlin70
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Finding Ultraconserved elements between human and zebrafish
... Hi all, I am looking to find ultraconserved elements between human and zebrafish. I understand multiple genomes (including these species) have already been aligned and ultraconserved elements have been identified. For example Miller et al. 2007. Is there a website where I can download a list of ul ...
ultraconserved elements comparative genomics written 2.7 years ago by ddowlin70 • updated 2.7 years ago by Chirag Nepal2.2k

Latest awards to ddowlin

Popular Question 10 months ago, created a question with more than 1,000 views. For Trinity run failed -- Phase 1
Popular Question 10 months ago, created a question with more than 1,000 views. For STAR aligner -- Alignment.out.sam missing
Popular Question 10 months ago, created a question with more than 1,000 views. For Trinity run failed -- Phase 1
Popular Question 18 months ago, created a question with more than 1,000 views. For Trinity run failed -- Phase 1
Popular Question 18 months ago, created a question with more than 1,000 views. For How to scale a cladogram to reflect branching time?
Popular Question 18 months ago, created a question with more than 1,000 views. For STAR aligner -- Alignment.out.sam missing
Popular Question 22 months ago, created a question with more than 1,000 views. For Trinity run failed -- Phase 1

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