User: al-ash

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al-ash20
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New User
Location:
European Union
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14 hours ago
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2 years, 8 months ago
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Posts by al-ash

<prev • 43 results • page 1 of 5 • next >
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Comment: C: Tune criteria for extraction of consensus sequence from bam/sam alignment
... Hi Prakki, that sounds a bit more suitable task for the combination of samtools and bcftools I gave above (after possibly tuning the parametres) - did you try to play with these tools? Or you might give a try to e.g. FastaAlternateReferenceMaker (https://software.broadinstitute.org/gatk/documentati ...
written 17 hours ago by al-ash20
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Comment: C: gff3 to CDS fasta
... As I understand the question of n.caillou, he wants to extract coding sequences, not transcript sequence (i.e. he needs to paste together exons for multi-exon genes)... ...
written 5 days ago by al-ash20
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Answer: A: Pyfasta Split By Header
... See https://pypi.python.org/pypi/pyfasta/ split the fasta file into one new file per header with “%(seqid)s” being filled into each filename.: $ pyfasta split –header “%(seqid)s.fasta” original.fasta You need to specify that sequence id (= the name of your fasta within multifasta file) wil ...
written 12 days ago by al-ash20
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Answer: A: How to trim nucleotide sequences to length divisible by 3
... I'm not sure what is the correct protocol for answering my own question. In the end, my input were multiple fasta files each including one sequence. I used `bioawk` and the `awk` modulo function (`%`) to create 3 cathegories of sequences: with sequence length divisible by 3, divisible by 3 with rem ...
written 27 days ago by al-ash20
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How to trim nucleotide sequences to length divisible by 3
... I want to strip predicted nucleotide protein coding sequences of the last 1 or 2 bases which represent incomplete codon. The input is multifasta consisting of nucleotide protein-coding sequences in reading frame 1. Some of them are trimmed at various positions at the 3'end resulting in 1-2 3'end nu ...
incomplete codon awk written 27 days ago by al-ash20
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Comment: C: Preventing EMBOSS transeq from renaming sequences
... Apparently not only two pipes but a single pipe as well slows down `transeq` substantially (actually it did not finish), e.g. >EOG190W000W|Mat_12980 Removing or replacing the pipe with other character solves the issue and `transeq` finished with the same multifasta in a second. ...
written 4 weeks ago by al-ash20
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Answer: A: Mira 4 Mapping Error
... Include line parameters = COMMON_SETTINGS -NW:cmrnl=no in your manifest config file. Note that the string `COMMON_SETTINGS` is critical here. Writing just `parameters = -NW:cmrnl=no` as suggested here by Adrian and as seems the original error message to suggest gave me error: * Parameter ...
written 4 weeks ago by al-ash20
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Comment: C: BAM format file to FASTA alignment file
... Bcftools consensus command does: > Create consensus sequence by applying VCF variants to a reference > fasta file so I think that it is far from being straightforward to use this tool for obtaining the consensus of mapped reads which does not contain bases from the reference sequence - whic ...
written 4 weeks ago by al-ash20
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Comment: C: Reference Assembly - Mapping Reads To A Reference Genome
... Dear Joseph, I'm aware of the date of your original post, but anyways: did you manage to find a replacement for the original pipeline (the one using *bcftools view -cg -*)? I'm now struggling with similar task and following pipeline using bcftools call: samtools mpileup -ABuf reference.fasta ma ...
written 4 weeks ago by al-ash20
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Tune criteria for extraction of consensus sequence from bam/sam alignment
... I'd like to extract consensus of reads from a bam/sam file which would follow particular criteria: 1. The portions of reference which have 0 coverage are represented in the consensus as N 2. If there is at least single read mapping to a particular nucleotide, this nucleotide is retrieved ...
consensus vcfutils bam bcftools sam written 5 weeks ago by al-ash20

Latest awards to al-ash

Scholar 27 days ago, created an answer that has been accepted. For A: How to trim nucleotide sequences to length divisible by 3
Popular Question 4 months ago, created a question with more than 1,000 views. For How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
Supporter 5 months ago, voted at least 25 times.

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