Error in opening fastq.gz file
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2.2 years ago
Jakpa ▴ 50

Hello Everyone,

I want to perform Adapter trimming. After running this command,

flexbar --adapter-min-overlap 7 --adapter-trim-end RIGHT \
--pre-trim-left 13 --max-uncalled 300 --min-read-length 25 \
--target ~/RNASeq/rawDataTrim/UHR_1
--pre-trim-left 13 --max-uncalled 300 --min-read-length 25 \
--target ~/RNASeq/rawDataTrim/UHR_2
--pre-trim-left 13 --max-uncalled 300 --min-read-length 25 \
--target ~/RNASeq/rawDataTrim/UHR_3


I got this error:

ERROR: Could not open file /home/mlsi/RNASeq/rawData/UHR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz
ERROR: Could not open file /home/mlsi/RNASeq/rawData/UHR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz
ERROR: Could not open file /home/mlsi/RNASeq/rawData/UHR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz


When I opened my rawData dir, I saw that I have the files.

UHR_Rep1_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz


What am I doing wrong?

Regards,
Anthony

linux flexbar Fastq adapter-trimming • 703 views
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Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (text becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.

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Thank you for Educating me. Am new in this platform

noted henceforth

Regards,

Anthony

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2.2 years ago
Ram 38k

Your files have Mix1 in their names whereas your command uses Mix2. Unless I'm missing something, that needs to be fixed.

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Thank you for spotting out my error. I have done the corrections and now everything is perfect...

This was the cause of my problem why I had duplicates reads in my samples in the FeatureCounts. The alignment was wrongly done .

Thank you all.. Anthony

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