Admin: Pierre Lindenbaum
Pierre Lindenbaum ♦ 113k
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- Google Scholar Page
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Posts by Pierre Lindenbaum
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... validate your bam file.
what is the output of `samtools view -c file.bam` ?
if there is an error, it doesn't come from `index` but from your upstream workflow. ...
written 2 hours ago by
Pierre Lindenbaum ♦ 113k
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... If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
![Upvote|Bookmark|Accept][1]
[1]: http://i68.tinypic.com/2m2ykjr.png
...
written 23 hours ago by
Pierre Lindenbaum ♦ 113k
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... linearize your fasa file, sort and use joiin.
Not tested but it should be something like
join -t $'\t' -1 1 -2 1 \
<(cat query.file | paste - - | cut -c 2- | sort -t $'\t' -k1,1) \
<(sort subject.file) |\
tr "\t" "\n"
...
written 1 day ago by
Pierre Lindenbaum ♦ 113k
4
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... > So am missing something here ?
yes. The 'M' operator doesn't mean that there is a **perfect** match. It means that the two sequences are best aligned if the read and the ref are aligned at this position. You want the derived symbols of 'M' which are '=' (match) and 'X' (mismatch) . See the SA ...
written 1 day ago by
Pierre Lindenbaum ♦ 113k
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... it sounds like a great project ! ...
written 1 day ago by
Pierre Lindenbaum ♦ 113k
1
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... split the analysis per chromosome ...
written 1 day ago by
Pierre Lindenbaum ♦ 113k
1
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65
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... > reads mapped and paired
the input of the mapping was a set of two fastq files R1.fq and R2.fq from a paired end experiment
> reads properly paired?
reads R1 and R2 from the same segment are mapped on the same chromosome, at a good expected distance with the correct directions. see https: ...
written 2 days ago by
Pierre Lindenbaum ♦ 113k
0
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1
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87
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... > So I can include the whole htslib-project in my project
what does 'include the whole htslib-project in my project ' means ? are you talking about git submodules ? https://git-scm.com/book/en/v2/Git-Tools-Submodules
...
written 2 days ago by
Pierre Lindenbaum ♦ 113k
1
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...
`-Ihtslib` means there is a directory named `htslib` in your current directory and this directory a bunch of `*.h` files.
if this directory is not in the current working directory , search for it (someting like)
find / -type -f -name "sam.h" 2> /dev/null
(wait if you have a large server ...
written 2 days ago by
Pierre Lindenbaum ♦ 113k
3
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69
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... in sam.h:
/*! @abstract the read is mapped to the reverse strand */
#define BAM_FREVERSE 16
usage:
(aln->core.flag & BAM_FREVERSE) ...
written 2 days ago by
Pierre Lindenbaum ♦ 113k
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For A: Where Can I Get Annovar 'Refgene' Format?
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For A: tool for bam soft clipping reads within bed file regions
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For A: tool for bam soft clipping reads within bed file regions
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For Mapping Snps To Pathways
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For samtools 1.0 'index' : CSI index vs BAI index ?
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For A: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
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For A: tool for bam soft clipping reads within bed file regions
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