Tag: StringTie

Index of /~psgendb/doc/bioLegato/blreads

Name Last modified Size Description Parent Directory   –   SOAPdenovo2.hints.html 2019-05-04 15:52 3.9K   Trimmomatic.hints.html 2019-05-20 13:32 6.3K   Trinity.hints.html 2019-04-23 11:39 2.4K   adaptercheck.hints.html 2021-05-13 12:27 8.0K   adaptercheck.html 2021-05-12 17:45 4.9K   adaptercheck_output.png 2021-05-12 17:17 51K   fastq_pair.hints.html 2019-04-05 13:16 3.4K   gffcompare.hints.html 2018-07-18 14:05 3.2K  …

Continue Reading Index of /~psgendb/doc/bioLegato/blreads

iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data

Abstract Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input…

Continue Reading iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data

Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data.

Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data. 0 Hi all, asking for a colleague, I’m looking for human non-poly-A mRNA that would end with a specific pattern ( say CCGCAT ). is it possible to find this in a RNA-SEQ data ? (e.g: www.ncbi.nlm.nih.gov//sra?term=SRR059132…

Continue Reading Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data.

A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest

1. Edmonds, R. L. & Eglitis, A. The role of the Douglas-fir beetle and wood borers in the decomposition of and nutrient release from Douglas-fir logs. Can. J. Res. 19, 853–859 (1989). Article  Google Scholar  2. Hlásny, T. et al. Living with bark beetles: impacts, outlook and management options. In:…

Continue Reading A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest

Transcriptional noise detection and Salmon TPMs

Transcriptional noise detection and Salmon TPMs 1 Hello, I’m analysing RNA-seq data from two datasets (from healthy samples) and created a unique GTF file to identify new isoforms by using StringTie. Then I used Salmon to estimate their TPMs, but I have some questions hoping anyone can help me: 1)…

Continue Reading Transcriptional noise detection and Salmon TPMs

Pybedtools error sans

Pybedtools error sans 20-08-2021 pysam – Error when I install samtools for python on windows – i trying install pysam, pybedtools modules on python got error: ($i=1; $i[email protected] temp]$ conda install pysam bedtools hisat2 [ snip. However,…

Continue Reading Pybedtools error sans

Finding differentially expressed lncRNA

Finding differentially expressed lncRNA 0 Hi all, I’m trying to diff. expressed lncRNAs between two groups (of humans). I wanted to use the following pipeline: trimmomatic –> stringtie/cufflinks –> Cuffmerge/stringtie merge –> FEELnc to find lncRNAs. To find diff. expressed transcripts I want to use the following pipeline: trimmomatic –>…

Continue Reading Finding differentially expressed lncRNA