User: SMK

gravatar for SMK
SMK350
Reputation:
350
Status:
Trusted
Location:
Gentopia, Belgium
Last seen:
15 minutes ago
Joined:
2 years, 7 months ago
Email:
h******@gmail.com

Posts by SMK

<prev • 48 results • page 1 of 5 • next >
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Answer: A: How can I obtain specimen_voucher information for each accession number in a pyt
... Hi [sw.knudsen][1], `specimen_voucher` will be `record["GBSeq_feature-table"][0]["GBFeature_quals"][3]["GBQualifier_value"]`: ``` $ cat test.py from Bio import Entrez Entrez.email = "email@any_email.com" organisms=["Diaphus anderseni"] genes = ["H3"] specs = {} acclist = {} for org in organisms: ...
written 1 hour ago by SMK350
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Comment: C: Biopython problem again
... You're welcome, good luck! ...
written 3 hours ago by SMK350
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Answer: A: Biopython problem again
... Hi [psschlogl][1], How many sequences are there in your `alpha.faa` and `beta.faa`? If both contain one, it works for me: ``` $ cat data/alpha.faa >seq1 MLLPLRRVLLKAVRQHNFFSESHATSINTRKGLVLGVYEKQSDDEGILLTEAAASFDSSISGKLSEML PTEFANTIEQKLSPFAHKVTVHKRPQSWIESEQMGAFLSVSKGSEEPPVFLELHYKGSLDSAQP $ cat da ...
written 3 hours ago by SMK350
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Comment: C: Label selected genes in volcano plot from ggplot
... Nice tips! 👍 Thanks, zx8754. ...
written 7 hours ago by SMK350
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Answer: A: Label selected genes in volcano plot from ggplot
... Hi [saamar.rajput][1], See the answer from [benformatics][2] (credits goes to him), the key is to make sure your "Gene" is in character type instead of factor. ``` > results <- read.delim("example.txt", header = TRUE, stringsAsFactors = FALSE) > head(results) Gene Fold pva ...
written 9 hours ago by SMK350
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Comment: C: To get number of hits from blastp output file
... You're welcome. Try this: ``` (for i in *.tsv; do echo -ne "${i}\t" && awk '$3>=40{print $2}' ${i} | sort -u | wc -l; done) > output.txt ``` ...
written 10 hours ago by SMK350
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Answer: A: To get number of hits from blastp output file
... Hi [fex2][1], Try: ``` for i in *.tsv; do echo -ne "${i}\t" && awk '$3>=40{print $2}' ${i} | sort -u | wc -l; done ``` It should returns something like: ``` blast_out1.tsv 217 blast_out2.tsv 172 blast_out3.tsv 215 ``` [1]: https://www.biostars.org/u/48471/ ...
written 10 hours ago by SMK350
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Comment: C: snpEff output gets zero results for synonymous SNPs
... Hi felipead66, Please check out the "Effect prediction details" section on [Input & output files][1] from snpEff document. Starting from version 4.0 VCF output uses SO terms by default, so the classic "NON_SYNONYMOUS_CODING" is now "missense_variant", "initiator_codon_variant", and "stop_retain ...
written 10 hours ago by SMK350
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Comment: C: snpEff output gets zero results for synonymous SNPs
... You can add `-csvStats` when running snpEff: `java -jar snpEff.jar eff -csvStats snpEffoutput.csv snpEff_database snpEffinput.vcf > snpEffoutput.vcf`. There will be a section counting each effect in the csv: ``` $ grep -A24 "# Count by effects" snpEffoutput.csv # Count by effects Type , Count , ...
written 12 hours ago by SMK350
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Comment: C: Amino acid sequence from CDS information of gff file
... If the GFF format is correct, try [gffread][1] with `-y`: (`-y write a protein fasta file with the translation of CDS for each record`) ``` $ gffread -y proteins.fa -g Homo_sapiens.GRCh38.dna.chromosome.1.fa Homo_sapiens.GRCh38.96.chromosome.1.gff3 $ head proteins.fa >transcript:ENST00000641515 ...
written 12 hours ago by SMK350

Latest awards to SMK

Scholar 3 hours ago, created an answer that has been accepted. For A: Uploading data files to Webin upload area under Linux
Scholar 9 hours ago, created an answer that has been accepted. For A: Uploading data files to Webin upload area under Linux
Scholar 1 day ago, created an answer that has been accepted. For A: Uploading data files to Webin upload area under Linux
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Uploading data files to Webin upload area under Linux
Scholar 3 days ago, created an answer that has been accepted. For A: Uploading data files to Webin upload area under Linux
Scholar 4 days ago, created an answer that has been accepted. For A: Uploading data files to Webin upload area under Linux
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Uploading data files to Webin upload area under Linux
Scholar 8 days ago, created an answer that has been accepted. For A: Uploading data files to Webin upload area under Linux
Scholar 8 days ago, created an answer that has been accepted. For A: Uploading data files to Webin upload area under Linux
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Uploading data files to Webin upload area under Linux
Scholar 14 months ago, created an answer that has been accepted. For A: Uploading data files to Webin upload area under Linux
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Uploading data files to Webin upload area under Linux

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