trim scripts help

Hi,

May I know if anyone has used the trim tool (http://graphics.med.yale.edu/trim/), I am trying to use this tool, while the paired_end_trim.pl file in the repository can not download due to error. Would someone who used this help to share the file.

Thanks so much!

sequencing

• 1,036 views • link

updated 6.0 years ago by h.mon

• written 6.0 years ago by dew •

You may want to use a current/actively maintained and supported program for this task. bbduk.sh from BBMap suite or trimmomatic/cutadapt/fastp should all be excellent choices.

• 0 views • link

written 6.0 years ago by GenoMax

OK, thanks so much for your guidance!

• 0 views • link

written 6.0 years ago by dew •

0 answers

No answers yet.

More posts like this

NCI Genomic Data Commons gdc-rnaseq-tool
written 1.8 years ago by cthangav •

I'm trying to use this tool: https://github.com/cpreid2/gdc-rnaseq-tool using the provided test file: python3 gdc-rnaseq-tool.py Test_Manifest.txt But when I run this command no files get downloaded. …
recommend tools for scRNAseq cell type annotation
written 3.7 years ago by dew •

Dear all, May I know if there are recommended tools/webs for the cell type annotation? Say, I have the cell **expression matrix**, and want to …
Redundancy reduction of de novo transcriptome assemblies with Compacta?
written 5.3 years ago by Dunois •

I've been sweating over how best to reduce the redundancy in a *de novo* transcriptome assembled using `Trinity`. I found this tool called [`Compacta`][1] ([here's …
whole length hg38 genomic repeat annotation file
written 5.4 years ago by dew •

Hi, I am trying to do TE expression analysis, while for the TE annotation gtf file, the file download from the http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/, for the 3rd …
Looking for dbSNP b144 version vcf
written 6.5 years ago by Anon •

Hi, I'm trying to get the hg19 build 144 version (May 2015) of dbSNP (as listed [here][1]), in vcf format (`hg19/dbSNP/144_20150605/All_20150605.vcf.gz`). Has anyone kept this …
who can share the GATK PON file (better above 10 sample) , hg19 version?
written 7.5 years ago by dew •

Hi,dear all, we are using GATK Mutect2 to get the somatic mutations of the sample, while we have to create our own PON file, which …
STREAM for identifying cell type
written 8.1 years ago by kanwarjag

Has anyone used http://xcell.ucsf.edu/. I am trying to find how one can find cell identity from this tool. Its out put gives me p values …
Problem with Cell Designer compatibility with SBML (xml) files
written 10.2 years ago by myasemi15 •

Hi, I downloaded a model from this website : http://jjj.biochem.sun.ac.za/models/ the model is related to MAPK Pathway, I was trying to open the downloaded file, …
BedTools intersect - Segmentation fault
written 11.0 years ago by Maria333 •

Hi, Has anyone experienced the "segmentation fault" error while trying to use bedtools intersect option? I am trying to see overlap exons between 2 bed …
MetaPath R package for pathway enrichment
written 11.9 years ago by chenyangls •

Hi! Anyone has used the R package called MetaPath before? It looks like a handy tool for meta-analysis for pathway enrichment analysis, but has been …