User: tanukitries

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Posts by tanukitries

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Comment: C: Fastqc error: Cannot encode phred score
... Thank you for all your help. I'll try this. ...
written 11 weeks ago by tanukitries0
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Comment: C: Fastqc error: Cannot encode phred score
... I am not. I used your command above, sorting with samtools and using that to convert the resulting file to a fastq file. I have two bam files for this paired end sequencing run and I performed this sort and conversion on both files separately. I ran fastqc on them I am getting different errors for t ...
written 11 weeks ago by tanukitries0
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Comment: C: Fastqc error: Cannot encode phred score
... I sorted the bam file like this: samtools sort myfile.bam -o myfile.sorted.bam I converted the resulting sorted bam using bedtools: bedtools bamtofastq -i myfile.sorted.bam -fq myfile.sorted.fq Thank you for your time and help! ...
written 11 weeks ago by tanukitries0
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Comment: C: Fastqc error: Cannot encode phred score
... This is what I get Exception in thread "main" java.lang.AssertionError: ASCII encoding for quality (currently ASCII-33) appears to be wrong for input quality 16 for base A at l ines 1 and 3, position 1. Please manually set qin=33 or qin=64. @NB501288_371_HGFMMBGX7:1:11101:16319:1208#GG ...
written 11 weeks ago by tanukitries0
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Comment: C: Fastqc error: Cannot encode phred score
... I sorted the bam files (paired end run) and converted them to fastq and attempted to fun fastqc again. I'm getting another error that looks related to the phred scores: Analysis complete for 3180L_L1_1.sorted.fq Failed to process file 3180L_L1_1.sorted.fq java.lang.IllegalArgumentExce ...
written 11 weeks ago by tanukitries0
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Comment: C: Fastqc error: Cannot encode phred score
... Thank you. I heard back from the core and was told that these unmapped_barcodes represents the reads from the illumina control that basically don't match barcodes of my actual samples. I have two bam files, these were generated from a paired end sequencing run. I sorted the bam files (was told the ...
written 11 weeks ago by tanukitries0
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Comment: C: Fastqc error: Cannot encode phred score
... These are unaligned!** **Actually, just kidding? I used samtools to try to get some information about the bam file: samtools view -H L1_1_sequence_unmapped_barcodes_phix.bam @SQ SN:phiX LN:5386 @PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -f L1_1_sequence_unmapped_barcodes_phix.sam / ...
written 12 weeks ago by tanukitries0
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Fastqc error: Cannot encode phred score
... I'm new to the world of RNA sequencing analysis. I'm attempting to run qc on a couple of RNA sequencing runs. These were performed on an Illumina platform (NextSeq500). The files that were returned to us were bam files. When I attempted to run fastqc (0.11.5) I immediately got an error: Faile ...
rna-seq written 12 weeks ago by tanukitries0

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