User: jsneaththompson

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Posts by jsneaththompson

<prev • 12 results • page 1 of 2 • next >
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Minimum base quality for Pindel
... I've been trying to find out whether Pindel has a minimum base quality required for a base to contribute towards a variant call, but I haven't found anything by going through forums or looking at the Pindel user manual. I have been looking at the source code on github and found this section of code ...
variant calling next-gen pindel written 20 days ago by jsneaththompson0
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Comment: C: Soft-clipping of reads in Amplicon-sequenced data
... You're right, I was getting confused. Cutadapt is removing primer sequences, and according to others in the lab we have amplicons of varying size. Thanks for the help. ...
written 6 weeks ago by jsneaththompson0
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Soft-clipping of reads in Amplicon-sequenced data
... I have a variant calling pipeline which I use to process amplicon-sequenced fastq files; it uses cutadapt to remove the adapter sequences on either the 5' or 3' end, then performs alignment with bwa mem. The user guide for cutadapt states that > And if you use BWA-MEM, the trailing (5’) bases ...
amplicon alignment soft-clipping written 6 weeks ago by jsneaththompson0 • updated 6 weeks ago by christacaggiano20
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What do outlined reads in IGV represent?
... I've been looking at some of my NGS data in IGV, and I've found some reads that aren't given a block colour, but instead are outlined in blue. I can't seem to find an answer in the IGV docs, does anyone know what this colour scheme signifies? [I've attached a link to a picture by way of example][1] ...
alignment next-gen igv written 7 weeks ago by jsneaththompson0 • updated 7 weeks ago by Vijay Lakhujani1.2k
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Comment: C: Connor Deduplication - AttributeError: 'module' object has no attribute 'Alignme
... Connor is using pysam 0.7.5 ...
written 9 weeks ago by jsneaththompson0
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Comment: C: Connor Deduplication - AttributeError: 'module' object has no attribute 'Alignme
... Ah, fair enough. Yes I know some python. ...
written 9 weeks ago by jsneaththompson0
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Comment: C: Connor Deduplication - AttributeError: 'module' object has no attribute 'Alignme
... I managed to switch to pysam 0.8.4 with pip, but I'm still getting the same error message when I try to run Connor ...
written 9 weeks ago by jsneaththompson0
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Comment: C: Connor Deduplication - AttributeError: 'module' object has no attribute 'Alignme
... According to pip, I'm using v 0.11.2.2 Connor says it requires pysam>=0.8.4,<0.9.1, how would I go about changing the pysam version? ...
written 9 weeks ago by jsneaththompson0
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Connor Deduplication - AttributeError: 'module' object has no attribute 'AlignmentFile'
... I'm attempting to use [Connor][1] to deduplicate some bam files in my variant calling pipeline, but so far whenever I attempt to run Connor I get the following error message: 2017-07-17 10:32:28|ERROR|An unexpected error occurred 2017-07-17 10:32:28|ERROR|Traceback (most recent call last): ...
barcoding alignment deduplication connor written 9 weeks ago by jsneaththompson0
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Comment: C: Pindel and GATK AD Concordance
... Thanks for the advice! ...
written 3 months ago by jsneaththompson0

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