User: liorglic

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liorglic130
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Posts by liorglic

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Comment: C: construction of draft genome from the contigs
... OK, so if I understand correctly, it looks like you have decent coverage, but no paired-end info of any type. This means you can't really expect to do any scaffolding with just the data you currently have. How about using an existing assembly of another strain [like this one][1]? You could use a too ...
written 1 day ago by liorglic130
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Comment: C: Low percent of RNA-seq reads mapping
... Thanks again. There is no sign for adapter (or other) issues with the data. I also don't know about rRNA genes in yeast. What I did notice is that in one of the supplementary tables of the paper, it is indicated that a low % of reads were mapped uniquely (actually below 50%), so maybe I should ask t ...
written 4 days ago by liorglic130
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Answer: A: construction of draft genome from the contigs
... Hi, I have some experience with eukarypte genome assembly from Illumina reads, but I've never worked on viruses or Ion torrent data. Still, a few things to note. I'm not sure Trinity is the most suitable tool, since it is intended for transcriptome, not genome assembly (and does a great job at i ...
written 4 days ago by liorglic130
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Comment: C: Low percent of RNA-seq reads mapping
... Thanks for taking this deep dive into the data. I actually took them from [this paper][1]. In this study, both mRNA-seq and ribosome profiling (what they call footprint - FP) were performed, and as far as I understand, I used the mRNA data, so why would only part of the reads be eligible? [1]: h ...
written 5 days ago by liorglic130
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Comment: C: Low percent of RNA-seq reads mapping
... Thanks for the answer. This is the Qualimap "Number of mapped reads", which according to the manual is "total number of mapped reads (left/right in case of paired-end reads, secondary alignments are ignored)". I actually have 0 unmapped (SAM flag 4) reads. Can you explain a bit more about this "hara ...
written 5 days ago by liorglic130
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Low percent of RNA-seq reads mapping
... Hello, I am new to RNA-seq data analysis and need some help. I sampled 1,000,000 reads from a mRNA RNA-seq experiment of yeast ([SRR1177156][1]). The library is a single-end, forward-stranded one, with 50bp reads, sequencing the reference strain S288C at standard growth conditions. I then created ...
star rna-seq mapping written 5 days ago by liorglic130 • updated 5 days ago by Amitm1.8k
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Comment: C: Proportion of long-read sequencing out of all sequencing?
... Thanks, that's about what I expected, but let's wait and see if someone has some data, even if it's just one sequencing center or something like this. ...
written 12 days ago by liorglic130
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Proportion of long-read sequencing out of all sequencing?
... Hi, Is anyone aware of available and up-to-date information regarding the proportion of long read sequencing out of all sequencing performed? I am looking for something like "out of X bases sequenced in 2019, Y% were in long reads", or similar. I've been googling this for a while but couldn't fi ...
long reads written 12 days ago by liorglic130
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Comment: C: How to handle paralogs in pan-genomes?
... Thanks again. Indeed it looks like Roary directly tackles this issue and tries to solve it using Conserved Gene Neighborhoods (CGN, known in eukaryotes as gene syntenny). As for OrthoMCL, it does treat paralogs and orthologs differently, but as far as I could tell, there is no obvious option to for ...
written 20 days ago by liorglic130
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Comment: C: How to handle paralogs in pan-genomes?
... Thanks for the interesting answer. Can you suggest a tool that split paralogs out off clusters? I agree that the number of genes in a pan genome is not particularly meaningful, but would still argue that leaving paralogs within cluster will result in somewhat "incorrect" results, since paralogs will ...
written 21 days ago by liorglic130

Latest awards to liorglic

Scholar 6 weeks ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Scholar 8 weeks ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Removing small contigs from fasta files
Popular Question 4 months ago, created a question with more than 1,000 views. For Gene copies vs. gene paralogs - what's the difference
Popular Question 4 months ago, created a question with more than 1,000 views. For Gene copies vs. gene paralogs - what's the difference
Popular Question 5 months ago, created a question with more than 1,000 views. For Pysam (python) problem parsing BAM reference id
Scholar 12 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Popular Question 22 months ago, created a question with more than 1,000 views. For Where can I find a small NGS raw data set?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Pysam (python) problem parsing BAM reference id

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