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I'm concerned about the quality of my aligned reads, and additionally the method I found in other issues for possibly fixing it. I would like confirmation that I made the right choice based on the sta…
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Hi
We have used Star (version 2.7.9a) to map paired-end reads, and obtained the following Log.final.out file:
```
Started job on | Jul 06 08:01:20
…
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### Description of the bug
STAR produces 2 alignment report files: pairedLog.final.out and singleLog.final.out. When MultiQC is generating the report, instead of combining them, seems like it randoml…
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Dear heng, thanks for the fantastic tool. I have some questions, can I use minimap2 to align pair-end 150bp short reads to assembled contig of these short reads, how is the performance? Or do you hav…
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Dear Alex,
I am posting the info from log files I got post running mapping with STAR. I am surprised by the difference in number of reads reported between ReadsPerGene.out.tab file and Log.final.ou…
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Dear Alex,
Briefly (see X.Log.final.out for 2 reference genomes X below), I've gotten unmapped percentages of 99.83% and 99.27% in mapping ~200M reads (for 8 samples of 2 species) of shark to argua…
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As a result of the meeting on March 17, 2016, we are going to add a script to the pipeline that refines genotype assignments by collapsing the reference set to the sequences that map the most reads pe…
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Hey Rhys
I was wondering why the same long reads used for the metaflye assembly are being used for the spades hybrid assembly with Short reads that did not map to the long read assembly. Wouldn't …
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Hi,
I'm running isoquant for two species with a relatively small genome size ~400Mb and around 20M reads (35G of fastq).
After 1 hour of run, the analysis does not progress. Since I run this job …
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I'm trying to align a slew paired end 100 bp transcript sequences to a reference genome from NCBI with a gff (converted to gtf) file. However, my % of reads unmapped: too short is coming up in the 60%…