Hi guys =) I'm sorry if this is a repeat but I haven't been able to find an answer using the search field or google.
I am trying to edit a fastq file that has a corrupt line. The read in question is VH00362:5:AAAV5KTHV:1:1210:64850:6869 where the read is just a massive repeat – not the expected 110bp. I am trying to remove two lines from this file and asking around I've been told to use `sed` as in
```gzip -c file.fastq.gz | sed "45500973,45500974d" > new.fastq.gz```
but when I run `wc -l ` to check the number of lines the results are incoherent, as if it has deleted much more than the two lines I asked. Another issue that I'm seeing with this file is that every time I run `gzip` I get a `invalid compressed data--format violated` error, which tells me the file is corrupted but I'm doing my best to salvage whatever I can from the file as it is an irreplaceable sample.
Is there another way to simply delete these two lines? Any tool or command you could recommend? Any help is deeply appreciated.
I am trying to edit a fastq file that has a corrupt line. The read in question is VH00362:5:AAAV5KTHV:1:1210:64850:6869 where the read is just a massive repeat – not the expected 110bp. I am trying to remove two lines from this file and asking around I've been told to use `sed` as in
```gzip -c file.fastq.gz | sed "45500973,45500974d" > new.fastq.gz```
but when I run `wc -l ` to check the number of lines the results are incoherent, as if it has deleted much more than the two lines I asked. Another issue that I'm seeing with this file is that every time I run `gzip` I get a `invalid compressed data--format violated` error, which tells me the file is corrupted but I'm doing my best to salvage whatever I can from the file as it is an irreplaceable sample.
Is there another way to simply delete these two lines? Any tool or command you could recommend? Any help is deeply appreciated.
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