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Hi, I run the HERA using test data and got an error about bwa mem.
I run the code below and got an 1.pbs file,
perl $Working_Script/09-Qsub-Pair_Alignment.pl list_outer_pacbio.txt $Working_Script $q…
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BWA-MEM command not set proper pair flag，perhaps because BWA not infer insert size characteristics. Is there some ways or tools to revise the flag value , for example revise 81 to 83, mate revise 161 …
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I have noticed that insert sizes from BWA-MEM seem to start high at the beginning of a chromosome, and drop down towards the end. This isn't really an issue (feel free to close and ignore) but I wante…
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Thanks for your great work in developing Chromap, an ultrafast aligner for chromatin profile alignment!
In the paper, you mentioned that Chromap is much faster than popular aligners such as BWA-me…
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Hi,
I have mate-pair data and need to find SVs using your tool (SVachra). I can see in your previous answer that you have recommend to use bwa-mem for the alignment but I have highly doubt that bwa i…
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Hi everyone
Currently, I am analyzing circRNAs from an RNA-Seq dataset using CIRI2 tools, following the steps outlined in the CIRI-cookbook. Here's how I have proceeded:
1. Checked the FastQC of t…
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Bug report by @irosenboom
It was reported for 2x150bp Novaseq reads that bwa mem performed alignments with extensive softclipping.
For example, some alignments were of 18bp with 82 bp simply so…
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Similar to https://github.com/bwa-mem2/bwa-mem2/issues/5 when aligning my dataset with bwa 0.7.17-r1188 and compare it with bwa mem2 (avx2 version), I get slightly different results.
```
(base) [p…
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# Click through:
1. Suppose you are starting at a BRC-analytics page listing available genomes:
2. No…
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Thanks for your excellent tool.
Previously I used vamb 3.0.2 for data analysls.
Currently I'm trying to run the latest version of vamb4, but unfortunately met such Runtime Error which I haven't figu…