Index out of range error for mouse Enterocyte_High_M1 data SRX7756509

[Divya6805]

There is an index out of range error while processing mouse Enterocyte_High_M1 data with the given pipeline. This error does not occur while using the test data provided along with the pipeline. Also, where can the sample barcodes used for all the experiments be accessed. It is not provided in the paper. Please help!

[ljwharbers]

Hi,

I'm sorry to hear you're having issues running the pipeline.
Unfortunately, people that developed and worked on this pipeline in the lab have moved on and nobody is actively working on this.

However, I did have a little bit of experience of running this (a few years ago) and have seen this same error. I just went back to some documentation and in my case it was related to the read name of the fastq file being formatted in a different way than the fastq files from the test dataset (especially when downloading SRR files from ENA/other repositories I believe).

Please have a look at the formatting of both read names of your fastq file and the test file. I recall having to remove the space in the read name, and replacing it with 6 (?) colons :. Such as (untested, please make sure you only edit the read name and nothing else).

zcat {sample}.fastq.gz | sed 's/ /::::::/g' | gzip > {sample}_fixed.fastq.gz

We will come back to you regarding the list of sample barcodes.

Sorry I couldn't be of more help.
Best,
Luuk

[Divya6805]

This worked ! Thankyou !

Best,
Divya