Hello,
I want to create fastq files by merging ".unmapped.fastq.gz" and ".accepted_hits.sort.coord.bam" files in syn7416949. I know that most of the fastq files were actually created and listed here syn8612191, but I need some additional files which are not found in here (syn8612191).
Some of the unmapped.fastq files listed here (syn7416949) are not in human readable format.
In this thread https://www.synapse.org/#!Synapse:syn2580853/discussion/threadId=7257&replyId=22920, it was said that for those kind of files, name should be changed as unmapped.fq.gz. I use this approach and it works on my Windows computer. But when I use the same approach in HPC cluster (Linux), those files are still in human non-readable format. Also, I tried to make those conversions in Windows computer and then transferred those files into HPC cluster but results didn't change, they are still human non-readable. When I ignore those problems, defected fastq file is forming and it fails in downstream processes.
Those are some of the samples that I encountered with this problem:
BM_36_389
BM_36_415
BM_36_284
BM_36_324
BM_36_325
BM_36_407
BM_36_330
I am open to any suggestions, and I hope you can help me to solve this problem.
Kind regards,
Atilay
Created by Atilay Ilgun Atilay Hello @abby.vanderlinden and @wpoehlm,
Thank you so much for responses. Thanks to @wpoehlm , I realized that I was using the wrong function to view the files. Problem is solved.
Thank you so much.
Atilay Hi @Atilay,
I do recall that there were some compressed files that did not have the '.gz' file extension as they should. As you suggested, the solution was to treat them as gzipped files even though the file name does not have the right extension. I didn't have any issues running the `zcat` command with any of the files when I processed this dataset, and I just downloaded a couple of the unmapped fastq files from the samples that you listed above and didn't have an issue running zcat to view the files. Which command specifically are you using to view the files on your cluster?
Thanks,
Will Hi Atilay,
That's strange that the name-change approach works on Windows but not your Linux cluster. @wpoehlm, do you have any suggestions as to what might be causing this format incompatibility?
It looks like in the folder syn7416949, most of the fastq files have suffixes of "unmapped.fastq.gz", while a handful are just "unmapped.fq". I wonder if that is related to the issue here, or just a coincidence?
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