User: serpalma.v

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serpalma.v10
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Germany
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13 hours ago
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4 years, 9 months ago
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Posts by serpalma.v

<prev • 42 results • page 1 of 5 • next >
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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 11 days ago by serpalma.v10
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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 11 days ago by serpalma.v10
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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 11 days ago by serpalma.v10
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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 11 days ago by serpalma.v10 • updated 11 days ago by ATpoint6.6k
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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 28 days ago by serpalma.v10
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Comment: C: Adding read group to bam files from multiplexed samples
... I read [here][1] that keeping bams separated during pre-processing is reasonable. And also, the way I understood it, for each sample, every bam file corresponds to a different read group, as they are derived from reads produced by different lanes. [1]: https://gatkforums.broadinstitute.org/gatk ...
written 29 days ago by serpalma.v10
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Adding read group to bam files from multiplexed samples
... Hello I have 60 samples (samp1...samp60), each one was barcoded and then pooled (10 samples/pool, 6 pools). Each pool was sequenced in 9 lanes. This leads to 1080 fastq files ( 60 samples * 9 lanes * 2 (PE) ) and 540 bam files. I want to do variant calling with GATK. I went through these two ...
gatk picard bam written 29 days ago by serpalma.v10
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Comment: C: Fix per tile sequence quality?
... Thanks, do you have an idea why are there so much less tiles in the y-axis than tiles in the flow cell? ...
written 6 weeks ago by serpalma.v10
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Fix per tile sequence quality?
... I see the following FastQC results in the "Per tile sequence quality" module: https://ibb.co/he9DBd Compared to other threads and articles I have seen, this does not look so bad in comparisson, but I am not sure if I should try to fix it anyway, files have been already run through Trimmomatic for ...
dnaseq quality control fastqc illumina written 6 weeks ago by serpalma.v10 • updated 6 weeks ago by genomax54k
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kmer content changes after trimming and removing adapters from reads
... Dear community I have a large set of FASTQ files from genomic DNA. I ran them through FastQC and found that the modules "overrepresented sequences" and "Kmer content" failed. The rest of the modules did not fail, except a warning in "Per tile sequence". Such pattern was present in almost all FASTQ ...
trimmomatic dnaseq fastqc written 6 weeks ago by serpalma.v10

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