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Scaffolding contigs generated by minia

genome assembly denovo_assembly minia scaffolding written 2.3 years ago by Mostafa • 20 • updated 2.3 years ago by _r_am ♦ 32k

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Finding fragemented transcriptome

denovo_assembly transcriptome written 3.6 years ago by EVR • 570 • updated 3.6 years ago by Rohit • 1.4k

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Recent Replies

C: Why did I get very poor scRNAseq files through STARSolo, Galaxy. by Youyy • 0
Thank you. I am not sure how to extract the code from Galaxy. Last time I didn't pair the R1 and ...
C: Why did I get very poor scRNAseq files through STARSolo, Galaxy. by Youyy • 0
I didn't pair my R1 and R2 files, I uploaded them separately, I am not sure if this is a case. I ...
C: Merging bowtie output by ATpoint ♦ 44k
Hello, I am not quite sure I understand. So you want to remove reads of mt origin from this paire...
C: How to avoid building millions of BWA indices? by GenoMax ♦ 94k
If the episome references are non-overlapping then I don't think you can `merge` the BAM files si...
C: Pairwise2 Alignment Gap Penalties by trinityduke100 • 0
Yes but is this for substitutions(mismatch) errors? I have a particular sequence that is passed...
C: RNA-Seq, HTSeq-Counts, counts are ~1M less compared to the reference research pa by xytwwwww • 0
Thank you for your reply! Also, ~1M loss in ~20M sounds very minor to me, would you agree on this?
C: trimming of fasta file by harry • 10
In previous questions, I asked about how to cut a sequence and rejoin. means cut in 2 equal parts...
C: Merging bowtie output by Mark • 840
Use the `samtools merge` to merge the bam files. Do not sure `cat` command.
A: How to convert phylo object to hclust object in R by engelbert_buxbaum • 0
Approach the problem from the other end: dist.dist <- as.dist(dist) DNA.hc <- hclu...
C: Getting alignments with lower scores on Biopython by trinityduke100 • 0
So essentially I have to find all the paths from the right bottom corner to the top left corner? ...
C: Stringtie transcripts to Gene Name by vkkodali • 2.4k
If you use a reference annotation file (`-G` parameter) at the time of transcript assembly using ...
C: How to avoid building millions of BWA indices? by Mark • 840
if this is about merging bam files, then samtools has the subcommand `merge`: http://www.htslib....

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