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Comment: Trimmomatic running but files containing purged reads are empty
by
GenoMax
142k
> Why is trimmomatic not removing any reads?
It is not mandatory that your data have extraneous/adapter sequence. If no extraneous sequenc…
Comment: FastQC interpretation - 16S sequencing
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GenoMax
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Since a specific region is being amplified it is expected that many of the library fragments will have identical sequences. Thus the low nu…
Comment: FastQC interpretation - 16S sequencing
by
Christopher
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@genomax Thank you so much for replying. I was quite unsure about the qualities. One more question. There is no problem within nucleotide d…
Comment: FastQC interpretation - 16S sequencing
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GenoMax
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> My specific question is about the feasibility of per base sequence content analysis and whether I should be concerned about a particular …
Comment: How to get the ratio of allele counts from GATK derived VCF file?
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anikcropscience
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But I used the same bam files in both freebayes and GATK. Even the overlapping SNPs from both software are giving different estimates in te…
Comment: How to get the ratio of allele counts from GATK derived VCF file?
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may be downsampling(?), QC failing reads ?
Comment: How to get the ratio of allele counts from GATK derived VCF file?
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anikcropscience
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Thank you. However, I extracted the AD for each SNP that gives two numbers separated by a comma. I guess the first one is for reference and…
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> However, I am doing SNP calling using GATK, but there is no such information field for reference and alternate allele counts.
it's in …
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> The index file is older than the data file: alignment.sorted.bam.bai
I don't think that warning is going to cause any issues. Not sure w…
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can you please retry, but add
rm -vf alignment.sorted.bam.bai
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if the CRAM/BAM is paire-end, it **must** be sorted on query name using samtools collate
https://x.com/lh3lh3/status/1132756684789768202
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machaalani29
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one of the issues is that I am not very sure how the sequencing was done, but I think it was single end.
any suggestions hoot do that?
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Possibly. You appear to have written the data to a single file (in case it was paired-end to begin with). Check to make sure secondary alig…
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https://www.biostars.org/u/18990/ : Please do not delete threads that have received a comment/answer.
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