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Renaming multiple paired files, deleting varying barcode character string in middle?

.everyoneloves__top-leaderboard:empty,.everyoneloves__mid-leaderboard:empty,.everyoneloves__bot-mid-leaderboard:empty{ margin-bottom:0;
}

0

I have a bunch of paired files with unneeded barcode tags within the middle of the file

.

I need to get rid of the barcode (which varies throughout the files) without modifying identifiers at the beginning or end of the file.

I have tried writing a script myself from what I've read online, but it appears to be a relatively poor attempt (screenshot of script attached)

Here's the error message I get when I try to run it:

Note that there are two types of error messages, first one I get, but I don't have duplicate file names in this folder so not sure why the second one is coming up.

Ideally, my final file name would be, for example:

LIB008983_TRA00020136_L001_R1.fastq.gz
LIB008983_TRA00020136_L001_R2.fastq.gz
LIB008983_TRA00020137_L001_R1.fastq.gz
LIB008983_TRA00020137_L001_R2.fastq.gz
..
..

and so on

Any pointers on how to do this? Any help/links would be appreciated.

shell-script awk

share|improve this question

asked 10 mins ago

ezhang1ezhang1

1

New contributor

ezhang1 is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

add a comment | 

0

I have a bunch of paired files with unneeded barcode tags within the middle of the file

.

I need to get rid of the barcode (which varies throughout the files) without modifying identifiers at the beginning or end of the file.

I have tried writing a script myself from what I've read online, but it appears to be a relatively poor attempt (screenshot of script attached)

Here's the error message I get when I try to run it:

Note that there are two types of error messages, first one I get, but I don't have duplicate file names in this folder so not sure why the second one is coming up.

Ideally, my final file name would be, for example:

LIB008983_TRA00020136_L001_R1.fastq.gz
LIB008983_TRA00020136_L001_R2.fastq.gz
LIB008983_TRA00020137_L001_R1.fastq.gz
LIB008983_TRA00020137_L001_R2.fastq.gz
..
..

and so on

Any pointers on how to do this? Any help/links would be appreciated.

shell-script awk

share|improve this question

asked 10 mins ago

ezhang1ezhang1

1

New contributor

ezhang1 is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

add a comment | 

I have a bunch of paired files with unneeded barcode tags within the middle of the file

.

I need to get rid of the barcode (which varies throughout the files) without modifying identifiers at the beginning or end of the file.

I have tried writing a script myself from what I've read online, but it appears to be a relatively poor attempt (screenshot of script attached)

Here's the error message I get when I try to run it:

Note that there are two types of error messages, first one I get, but I don't have duplicate file names in this folder so not sure why the second one is coming up.

Ideally, my final file name would be, for example:

LIB008983_TRA00020136_L001_R1.fastq.gz
LIB008983_TRA00020136_L001_R2.fastq.gz
LIB008983_TRA00020137_L001_R1.fastq.gz
LIB008983_TRA00020137_L001_R2.fastq.gz
..
..

and so on

Any pointers on how to do this? Any help/links would be appreciated.

shell-script awk

share|improve this question

asked 10 mins ago

ezhang1ezhang1

1

New contributor

ezhang1 is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

share|improve this question

asked 10 mins ago

ezhang1ezhang1

1

New contributor

ezhang1 is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

share|improve this question

asked 10 mins ago

ezhang1ezhang1

1

New contributor

ezhang1 is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

asked 10 mins ago

ezhang1ezhang1

1

New contributor

ezhang1 is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

asked 10 mins ago

ezhang1ezhang1

1