User: serpalma.v

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serpalma.v20
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Germany
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Posts by serpalma.v

<prev • 47 results • page 1 of 5 • next >
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Comment: C: Per base GC content with a shoulder after adapter removal and trimming
... The sample was already processed with trimmomatic, including adapter removal. FastQC did not detect adapters. The quality Phred score was above 28 for all bases. ...
written 12 days ago by serpalma.v20
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Comment: C: Per base GC content with a shoulder after adapter removal and trimming
... I added that to the post. It is WGS data ...
written 12 days ago by serpalma.v20
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Per base GC content with a shoulder after adapter removal and trimming
... Hello! The following graph shows a fastq file (WGS) after trimming (sample comes from mouse). Adapters and low quality bases were removed with trimmomatic. The module "Overrepresented sequences" was flagged with a "PASS". I have gone through other threads. This one in particular help me [link1][1] ...
gc content fastqc written 12 days ago by serpalma.v20
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Comment: C: what is the conventional apporach to calculate depth of coverage?
... In which case then `read depth` would be equivalent to option A and `coverage` would be equivalent to option D. would you agree? ...
written 5 weeks ago by serpalma.v20
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what is the conventional apporach to calculate depth of coverage?
... Hello for WGS, when a given depth of coverage is recomended, for example: 30x for variant calling, where does that quantitiy derive from?: A/ from raw reads (number of reads * read length / genome size) B/ from raw reads minus the duplicate percentage. ( (number of reads-%duplication) * read leng ...
wgs dnaseq coverage snp depth written 5 weeks ago by serpalma.v20 • updated 5 weeks ago by finswimmer6.2k
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Comment: C: Which indication of a failure can be found in bwa-mem or samtools' output?
... Thanks, If I understood correctly, I will have to re-run the script including the exit status after bwa and samtools, did I get it right? ...
written 9 weeks ago by serpalma.v20
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Comment: C: Which indication of a failure can be found in bwa-mem or samtools' output?
... Beginning and end for the first pair: [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 2210544 sequences (320000246 bp)... [M::process] read 2207480 sequences (320000211 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (82, 871436, 27, 24) [M ...
written 9 weeks ago by serpalma.v20
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Comment: C: Which indication of a failure can be found in bwa-mem or samtools' output?
... I did this `nohup script.sh &> script.out &` ...
written 9 weeks ago by serpalma.v20
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Which indication of a failure can be found in bwa-mem or samtools' output?
... Hello I aligned 108 FASTQ pairs with bwa-mem in one go, after alignment I transformed the SAMs into BAMs with samtools. I wrote the script so that I know when a pair starts and ends. The job was completed, because I found 108 BAMs in the output directory and the script indicates that all pairs wer ...
samtools bwa written 9 weeks ago by serpalma.v20 • updated 9 weeks ago by ATpoint8.0k
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Comment: C: Adding read group to bam files from multiplexed samples
... so then the read groups should be as follows: - ID: samp31 - SM: samp31 - PL: ILLUMINA - LB: samp31 Not sure about keepin PI and PU now... Correct? ...
written 12 weeks ago by serpalma.v20

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