![]() Simply running less file.fq.gz (with your filename obviously) and seeing if there's something strange at the beginning, or whether the file even looks like a fastq file is a good start.Ĭhecking that the whole file can decompress correctly is also good. Using the less program to look at the start of your file to see if there's anything weird there. ![]() Depending on what the nature of the corruption is in your data there may be a nice command line option to fix it (ie skipping the first few lines), but there's so many ways that a fastq file can be messed up that it's difficult to suggest a general solution. Most editors are not designed to deal with files which are that big, nor can they cope with compressed files. You are now back to the terminal and you can type the following in order to check that the line has been removed:īut in the fastq file, while we are doing analyses we can't erase by ourself just like that, right?Įditing huge fastq files is not trivial. ^x (to quit nano you will be prompted to save the file if not done before) Thus, the read is now on line 2 of the file ^c (to indicate that the cursor position is here) Move within the file using keyboard arrows to go on the symbol where the first read starts ![]() Then, type the following command to open the file (it takes a while): In the linux terminal, go to the directory where your fastq file is located (using the cd command).I am writing here how to use it, if it can help others save time! I also had to delete a blank line at the end of the fastq file.Īs I hadn't used nano before, it took me some time to use it properly. It was something like a path to a server where the file was stored by the user. So I knew it was not data corruption, and I could delete it. The string of characters that was before the first read was not from the raw data but was added afterwards. So you means fastqc cannot find which line is corrupted and I must find other tools to fix the problem? HI am sorry but the blank in the first line is caused by myself when i copied it from terminal to this issue.I am very sorry it caused your misunderstanding.And the real first part file shows data is rawdata without any process. Run it and it shows the just attached the first part but how can I know which line is corrupted? or how do fastqc deal with such problems?or I must use other qc tools?Thank you so much in advance.
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