Paul Cantalupo

Hello, I tried to run the pipeline (`-r dev`) into accepting additional Guppy parameters so that Guppy would perform Qscore filtering of fastq into "pass" and "fail" groups. However the...

how do I hide autocrine (self to self) communication in netVisual_bubble?

1

Hello, trying to visualize the communication between two celltypes in both directions (i.e. T Cell -> Macrophage and Macrophage -> T Cell). My code is: ``` sources = c(5,8) #...

Hello, I ran the nfcore differentialabundance pipeline (v1.4.0) on 4 samples (2 Control and 2 Experimental). The shiny app seems to work for all other functionality except when I run...

how do you get all the potential processed transcripts

1

Hello, I'm trying to find novel transcripts so I don't use the -e option. Using the verbose option, I see in the output that it says `[10/07 16:20:42]^bundle NC_001538:1-5153 done...

can't run viruspy with data not in the SRA database

2

This issue is for those who want to run viruspy against sequences that are not in the SRA database. A clear case for this is somebody that did their own...

Not really an issue but something to remember. MagicBlast version 1.2 by default does not return unaligned reads. HOWEVER, version 1.3 does return unaligned reads by default. To turn this...

Aborted core dumped error

2

Hello, I ran Squid v1.5 using 12 cpus and 96 GB RAM with the following command: `squid -b AUR1.Aligned.sortedByCoord.out.bam -c AUR1_chimeric_sorted.bam -o AUR1.squid.fusions` Here is the output and it was...

I tried installing the [standup script](https://github.com/BlockchainCommons/Bitcoin-Standup-Scripts/blob/master/Scripts/LinodeStandUp.sh) following your [directions](https://github.com/BlockchainCommons/Learning-Bitcoin-from-the-Command-Line/blob/master/02_1_Setting_Up_a_Bitcoin-Core_VPS_with_StackScript.md#21-setting-up-a-bitcoin-core-vps-with-bitcoin-standup). I noticed that the HiddenService lines were not added to my `/etc/tor/torrc`. Then, I saw this error in `/standup.err`: ``` standup@localhost:~$...

no 'build' directory found on skesa branch in tools/skesa

5

Hello, I'm trying to install skesa. I cloned the repo as per README.md. Then had to checkout the skesa branch (which is not in the readme). Now I cannot find...

import() does not handle multiple tag attributes

1

Hello, I'm trying to import the following very simple GTF file with 1 line (comes from Gencode v38 GTF [here](http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.annotation.gtf.gz)) that has multiple `tag` attribues: ``` $ cat multipletag.gtf chr6...