User: Fabio Marroni
Fabio Marroni • 1.3k
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Posts by Fabio Marroni
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... Hi!
The example file is hard to read for me. Maybe you can format it somehow?
Regarding your choices, I suggest doing a mix.
Doing everything with the same approach is suggested, otherwise you will never knwo if the differences are real or due to different analysis options.
However, assuming that ...
written 10 days ago by
Fabio Marroni • 1.3k
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... Mmmm... then I suggest you give a look to [stacks][1]. It is a widely used software for analyzing RAD-seq data. HAving RADseq, you can "easily" assemble the small loci using stacks. The manual explains how to do that. I am not sure on how to best manage pooled data, I never had to do that with stack ...
written 14 days ago by
Fabio Marroni • 1.3k
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... Try to spot the differences between one of the families that are analysed and one of those that are not. Maybe you can select the smallest and show the files here. I usually had no problems with merlin. ...
written 15 days ago by
Fabio Marroni • 1.3k
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... What do you mean by pool seq data? Did you amplify one region of the genome and sequence it in a large number of pooled subjects? Are you interested in genome-wide SNPs or SNPs in a selected region? ...
written 15 days ago by
Fabio Marroni • 1.3k
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... What is in the file: out_PAAD_small.seqz.gz?
Try and see if all the chromosomes are in the file.
I tried sequenza on the test data set and it worked fine, so it is possible that there is a problem with the input. ...
written 17 days ago by
Fabio Marroni • 1.3k
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Comment:
C: DESEQ2 for ASE
... Theoretically it should be legitimate, provided you correctly accounted for all the possible mapping bias you might have when dealing with allele specific expression. However, you can also use some software developed for ASE, such as [allim][1]. I don't know if you are expert in ASE, but in case you ...
written 19 days ago by
Fabio Marroni • 1.3k
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Comment:
C: Bwa producing no alignment
... mmm, yes, I noticed you have `#` in the quality, which cannot be Illumina 1.3+ nor 1.5+.
1) Why do you think it is something in the quality? Did you receive some warning?
2) Have you tried building a small reference identical to one of your reads and aligning against it?
...
written 21 days ago by
Fabio Marroni • 1.3k
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Comment:
C: Bwa producing no alignment
... Is it possible that you have quality in Illumina 1.3+ or 1.5+ while (I think) bwa is now expecting Illumina 1.8+? Try giving a look at these posts:
https://www.biostars.org/p/43631/
https://www.biostars.org/p/87958/
https://en.wikipedia.org/wiki/FASTQ_format ...
written 22 days ago by
Fabio Marroni • 1.3k
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Comment:
C: Bwa producing no alignment
... Just out of curiosity: why are you running aln and index at the same time?
For what I remember aln is used to align and should create a sai output, while index is used to create an index of a fasta reference file. ...
written 22 days ago by
Fabio Marroni • 1.3k
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... Indeed, I deleted my comment after realizing that you already mentioned that you read the paper and manual! ...
written 22 days ago by
Fabio Marroni • 1.3k
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For A: What Is Ivsi Number Of A Mutation?
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For A: what does Num_Probes in a segmentation file refer to?
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For A: what does Num_Probes in a segmentation file refer to?
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For Bwa-Mem: Discriminate Between Reads Mapping Uniquely And Those Mapping In Multiple Positions
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For A: what does Num_Probes in a segmentation file refer to?
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For C: How To Find Rna-Seq Data Of Published Papers?
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For C: How Large Can A Coverage Discrepancy Be Between Two Aligners, Specifically Bwa A
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