User: guillepalou4

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Posts by guillepalou4

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Comment: C: kraken: unable to download the databases from ncbi
... Thank you for the help! ...
written 5 weeks ago by guillepalou40
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Comment: C: kraken: unable to download the databases from ncbi
... Hello Sed Modha, I have been using your script but at some point the following error appears: sys:1: DtypeWarning: Columns (20) have mixed types. Specify dtype option on import or set low_memory=False. Traceback (most recent call last): File "./UpdateKrakenDatabases.py", line 118, in ...
written 5 weeks ago by guillepalou40
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Comment: C: How to sort an interleaved fastq file by the barcode (BX:Z:) from the header
... Amazing, now it works! Thank you so much! :) ...
written 6 weeks ago by guillepalou40
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How to sort an interleaved fastq file by the barcode (BX:Z:) from the header
... Hello guys! I interleaved R1.fastq and R2.fastq files into one file called interleaved.fastq, so that for each read pair, the R1 read in the file comes immediately before the R2 read, followed by the R1 read for the next read pair, and so on. In the header of the interleaved.fastq I also have some ...
barcode header interleaved fastq sort written 6 weeks ago by guillepalou40 • updated 6 weeks ago by Pierre Lindenbaum106k
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Comment: C: Sorting my .bam with samtools produces differences in the fastq files generated
... I see... Anyway I checked and both gives me the sequence and the quality lines respectively. It's strange, I will try again similarly today. Thanks for the help :). ...
written 6 weeks ago by guillepalou40
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Comment: C: Sorting my .bam with samtools produces differences in the fastq files generated
... Thanks a lot Devon. It showed me no results so I guess my files are correct. But I wonder if my command was wrong. I suppose it is! ...
written 6 weeks ago by guillepalou40
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Comment: C: Sorting my .bam with samtools produces differences in the fastq files generated
... It's probably... I used this command: cat R1.fastq | paste - - - - | cut -f 3 | tr -d '\n' | wc -m 1495694956 cat R1.fastq | paste - - - - | cut -f 5 | tr -d '\n' | wc -m 1494905216 Do you know another command that compares the length of each read to the length of the quality scores? Taking int ...
written 6 weeks ago by guillepalou40
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Comment: C: Sorting my .bam with samtools produces differences in the fastq files generated
... Thanks for the answer. I would prefer using *samtools fastq* to generate my fastq as It's the only tool I've found I can retrieve an specific TAG from the bam (I need to retrieve a BX: tag which is a barcode). Also I found this on BBMap: To discard reads that have mismatching lengths of bases and ...
written 6 weeks ago by guillepalou40
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Comment: C: Sorting my .bam with samtools produces differences in the fastq files generated
... Do you also know, why do I have different number of characters in the same R1 file for example, after using samtools fastq? I have 1495694956 number of nucleotides and 1494905216 number of quality scores. It doesn't make sense. ...
written 6 weeks ago by guillepalou40
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Comment: C: Sorting my .bam with samtools produces differences in the fastq files generated
... Oh, I didn't know that, thanks! I also checked the sorted vs unsorted bam and they have different number of lines. I wouldn't expect that. ...
written 6 weeks ago by guillepalou40

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