User: tanukitries
tanukitries • 0
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Posts by tanukitries
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... Thank you for all your help. I'll try this. ...
written 11 weeks ago by
tanukitries • 0
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... 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
tanukitries • 0
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... 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
tanukitries • 0
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... 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
tanukitries • 0
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... 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
tanukitries • 0
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... 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
tanukitries • 0
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... 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
tanukitries • 0
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... 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 ...
written 12 weeks ago by
tanukitries • 0
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