User: nikelle.petrillo

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Providence College, Providence, RI
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Posts by nikelle.petrillo

<prev • 81 results • page 1 of 9 • next >
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Comment: C: weird STAR output, bash scripting problem
... Yes, I thought of that but not sure how to incorporate `basename` into my existing code. ...
written 20 months ago by nikelle.petrillo100
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Comment: C: weird STAR output, bash scripting problem
... Thank you, but when I try this the output .bam file keeps getting written over. ...
written 20 months ago by nikelle.petrillo100
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Comment: C: weird STAR output, bash scripting problem
... I found the script online but modified it to try to fit my data. `echo $i` spits out values such as these: filtered.ABC4454232_1.1P filtered.ABC4454232_2.2P filtered.ABC4454233_1.1P filtered.ABC4454233_2.2P .... Which are the correct values, i guess i do not understand how to ...
written 20 months ago by nikelle.petrillo100
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weird STAR output, bash scripting problem
... Hi all. I am trying to align PE reads with STAR. I have trimmed files (used trimmomatic) that look like `*_1.1P.fastq.gz *_1.1U.fastq.gz *_2.2P.fastq.gz *_2.2U.fastq.gz` . I only want to align the` *_1.1P.fastq.gz `and` *_2.2P.fastq.gz` files. Here is my code: #!/bin/bash mkdir -p align ...
star rna-seq bash written 20 months ago by nikelle.petrillo100 • updated 20 months ago by h.mon24k
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Comment: C: automated script to trim paired end RNA seq reads using Trimmomatic
... I believe I got it to work by adding: `(basename -s .fastq.gz $f1)` so it strips off the suffix of $f1. Thanks for all the help. ...
written 20 months ago by nikelle.petrillo100
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Comment: C: automated script to trim paired end RNA seq reads using Trimmomatic
... that is very weird. I ran that exact script and this is what I got: ( i know the file names are different than 12345.1... just used that for simplicity. Maybe these different file names are the cause of the problem? ) CTG-0011_ACAGTG_AC62F2ANXX_L003_001.R2.fastq.gz filtered.CTG-0011_ACAGTG ...
written 20 months ago by nikelle.petrillo100
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Comment: C: automated script to trim paired end RNA seq reads using Trimmomatic
... Thanks for your reply! I do have another question regarding using the basename to get each file prefix. Your code outputs my files as: `filtered.12345.1.fastq.gz.1P.fastq.gz filtered.12345.1.fastq.gz.1U.fastq.gz filtered.12345.1.fastq.gz.2P.fastq.gz filtered.12345.1.fastq.gz.2U.fastq.gz` Is ther ...
written 20 months ago by nikelle.petrillo100
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automated script to trim paired end RNA seq reads using Trimmomatic
... Hi all, I am using an automated script to trim paired end fastq.gz files using Trimmomatic. I have this code: #!/bin/bash for f1 in *1.fastq.gz do f2=${f1%%1.fastq.gz}"2.fastq.gz" java -jar /Trimmomatic-0.36/trimmomatic-0.36.jar PE -trimlog TrimLog $f1 $f2 -baseou ...
trimmomatic loops trimming rna-seq written 20 months ago by nikelle.petrillo100 • updated 20 months ago by h.mon24k
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Downloading Fastq files from ENA using FTP
... Hi all, I would like to download all the .fq files used in the study PRJNA350777. Link is here: http://www.ebi.ac.uk/ena/data/view/PRJNA350777 How do I go about downloading all the .fq files from this study using FTP? Thanks for the help, Nikelle ...
fastq ena rna-seq download written 20 months ago by nikelle.petrillo100 • updated 20 months ago by genomax65k
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How to see what percentage of reads remain after quality filter to a certain phred score
... Hi all, I ran FASTQC on my raw reads to check out some quality stats. However, I would like to see how many reads will remain if i set the phred quality score to 30. Is there a way / a tool to do this? Thanks for the help! Nikelle ...
quality control phred rna-seq fastqc written 21 months ago by nikelle.petrillo100

Latest awards to nikelle.petrillo

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