User: jvire1

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jvire110
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Posts by jvire1

<prev • 17 results • page 2 of 2 • next >
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Comment: C: Pulling out gene names from a FASTA file with a list of IDs
... After I looked at the output more closely I realized that it isn't doing quite what I want it to. The beginning of the list of identifiers looks like this: Zpz_sc04830.1.g00020.1.sm.mk Zpz_sc04830.1.g00020.1.sm.mk Zpz_sc04830.1.g00020.1.sm.mk Zpz_sc04830.1.g00020.1.sm.mk Zpz_s ...
written 9 weeks ago by jvire110
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Pulling out gene names from a FASTA file with a list of IDs
... Does anyone know of a simple scripting solution to take a list of accessions and pull out the gene name from the header of FASTA sequences? For instance given the accession: XP_016469325.1 and given the FASTA entry: >XP_016469325.1 Nicotiana tabacum|C3H|C3H family protein MEEELLKRNTDCVYFLASPLTC ...
rna-seq written 9 weeks ago by jvire110 • updated 9 weeks ago by cpad01122.9k
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Comment: C: Scripting solution to generate a list of KEGG ORTHOLOGY (KO) terms from a tab-de
... Thank you! Worked like a charm. -James ...
written 9 weeks ago by jvire110
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Scripting solution to generate a list of KEGG ORTHOLOGY (KO) terms from a tab-delimited annotation file
... Does anyone happen to know a basic scripting (perhaps awk or python) approach to extracting KEGG orthology terms from a tab delimited annotation file? The file in question has rows that look look like this: TRINITY_DN18877_c0_g1_i1 KEGG:zma:103654828`KEGG:zma:103654829`KEGG:zma:542341`KO:K0299 ...
rna-seq written 9 weeks ago by jvire110 • updated 9 weeks ago by Sparrow_kop170
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Comment: C: GOterm enrichment for a single transcriptome assembly; using abundance counts an
... Thank you, I really appreciate it! I'll look into this approach and let you know how it goes. ...
written 4 months ago by jvire110
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Comment: C: GOterm enrichment for a single transcriptome assembly; using abundance counts an
... @Tran Kim Ngan Thank you for your suggestion. Unfortunately my abundance counts and GOterms are in separate files, while input into REVIGO requires GOterms and a meaningful variable (cumulative abundance counts for transcripts assigned a specific GOterm). I thought maybe a awk command could be used ...
written 4 months ago by jvire110
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GOterm enrichment for a single transcriptome assembly; using abundance counts and GOterms in TAB delimited form
... I am running into the issue that all of the GOterm enrichment tools I have found so far require differential expression data. Unfortunately I am working with a single transcriptome due to lack of funding. I have only been able to graph GOterms in terms of genes annotated, which doesn't seem all that ...
gene rna-seq written 4 months ago by jvire110 • updated 4 months ago by Tran Kim Ngan0

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