User: danekhoffman0319

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Posts by danekhoffman0319

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Comment: C: Issues with reading .bed files and compressing output in a specific format
... Unfortunately, I am limited to jupyter-lab at the moment, though I see your point. ...
written 5 days ago by danekhoffman03190
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Issues with reading .bed files and compressing output in a specific format
... import gzip input_file = open("example.bed","rb")#compress existing file data = input_file.read() with gzip.open("example.bed.gz", "wb") as filez: filez.write(data) filez.close() import pandas as pd#converts gz file to .txt df=pd.read_csv("example.bed.gz", d ...
bed python gzip written 5 days ago by danekhoffman03190 • updated 5 days ago by Alex Reynolds30k
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Comment: C: HTseq feature count handling of transcripts with shared exons?
... Thank you, this is what I suspected but I wanted a second opinion! ...
written 10 days ago by danekhoffman03190
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HTseq feature count handling of transcripts with shared exons?
... I am curious to know how htseq will assign a read to a particular transcript if said read maps to a shared exon between two isoforms? If anyone has any experience with this or can offer any insight it would be greatly appreciated. Thank you in advance. ...
htseq rna-seq dge written 10 days ago by danekhoffman03190 • updated 10 days ago by i.sudbery9.1k
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Resources for learning how to submit jobs in unix-based cluster
... I am interested in knowing if anyone can recommend any good resources for learning how to submit jobs on a unix based cluster. For example, I already have R scripts for aligning and performing DGE analysis that run on my computer but I would like to utilize the cluster for future analysis. Does anyo ...
cluster bioinformatics unix written 12 days ago by danekhoffman03190
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Mouse Tissue Specific Transcriptome Databases
... Does anyone know of any good mouse whole transcriptome databases that are organized by tissue? I am looking specifically for a database of mRNAs from mouse whole blood. ...
genome rna-seq written 22 days ago by danekhoffman03190
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Extracting Unmapped Reads from BAM files using Rsamtools
... Hello, Does anyone have any experience extracting unmapped reads from BAM files and converting them back to fastq format using Rsamtools? If you could provide some generic code to address this problem it would be greatly appreciated. I am mapping C. elegans RNA library against E. coli genome to re ...
R next-gen samtools rna-seq rsamtools written 9 weeks ago by danekhoffman03190 • updated 9 weeks ago by Shalu Jhanwar460

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