Moderator: finswimmer

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finswimmer4.5k
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Posts by finswimmer

<prev • 742 results • page 1 of 75 • next >
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Answer: A: Parsing large sequence file into per-sample files after barcodes/primers removed
... An `awk` solution: $ awk '$0 ~ "^>" {match($1, /^>([^_]+)_/, id); filename=id[1]} {print >> filename}' seqs.fna fin swimmer ...
written 13 hours ago by finswimmer4.5k
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Comment: C: Google search for gene variants
... What's your question/intention of this post? ...
written 15 hours ago by finswimmer4.5k
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Comment: C: multiIntersectBed Error: The requested bed file could not be opened. Exiting!
... I guess this more a limitation by the OS. On many linux distribution the maximum number of open files is 1024. You can find it out on your system with $ ulimit -n There seems to be many ways to increase the number if necessary, e.g. like [here][1] fin swimmer [1]: https://easyengine.io/t ...
written 15 hours ago by finswimmer4.5k
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Comment: C: Insert size smaller than the read lenght
... > Yes, because if you don't trim the adapters, the reads won't merge > anyway. AFAIK `bbmerge` can use the adapter information for merging. So don't trimming before merging increases the merging rate. fin swimmer ...
written 23 hours ago by finswimmer4.5k
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Answer: A: Extract SNPs from VCFfile located in genes based on GFF file information
... Use [bedtools][1]: $ bedtools intersect -a input.vcf -b genes.gff -header -wa > output.vcf --- **EDIT:** For (very) large `vcf` files it might be more efficient to `bgzip` and `tabix` index the `vcf` file, convert your `gff` to `bed` and use `tabix` to query the regions **1. bgzip and ind ...
written 1 day ago by finswimmer4.5k
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Comment: C: Alignment with BWA and SAMtools
... Hello Shello, now we are back to the questions I asked at the very [beginning][1]. And: What kind of sample is it? [1]: https://www.biostars.org/p/332056/#332080 ...
written 2 days ago by finswimmer4.5k
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Answer: C: How to concatenate multiple fasta file
... What about this (based on your header description [here][1])? $ cut -f1 -d "-" *.fa|awk -v RS=">" -v FS="\n" -v OFS="\n" '{for(i=2; i<=NF; i++) {seq[$1] = seq[$1]$i}}; END {for(id in seq){print ">"id, seq[id]}}' > combined.fa [1]: https://www.biostars.org/p/332853/#333193 ...
written 4 days ago by finswimmer4.5k
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Comment: C: Difference between | and || in filtering expressions by bcftools
... Hello pd3, thank you for your response. Unfortunately this isn't an answer to my initial question about the differences between `|` and `||`. As I [wrote][1] a little bit later the difference between `&` and `&&` is clearly explained in the manual, even if the description "&& ( ...
written 5 days ago by finswimmer4.5k
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Answer: A: Removing duplicate protein sequences from fasta file
... Use [seqkit][1]: $ seqkit rmdup input.fa > output.fa [1]: https://bioinf.shenwei.me/seqkit/usage/#rmdup ...
written 5 days ago by finswimmer4.5k
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Comment: C: How to concatenate multiple fasta file
... Could you please explain how the bacterias are delimited from the genes? ...
written 6 days ago by finswimmer4.5k

Latest awards to finswimmer

Scholar 1 day ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Good Answer 1 day ago, created an answer that was upvoted at least 5 times. For A: Extract SNPs from VCFfile located in genes based on GFF file information
Appreciated 1 day ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Scholar 1 day ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 6 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Appreciated 6 days ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Student 6 days ago, asked a question with at least 3 up-votes. For Why not merging?
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 6 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 12 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 15 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
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Scholar 19 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Appreciated 22 days ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Commentator 22 days ago, created a comment with at least 3 up-votes. For A: sam file error
Scholar 25 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
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Scholar 4 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
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Scholar 5 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file

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