Moderator: genomax

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genomax37k
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Posts by genomax

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Comment: C: Getting Error with bowtie2! "Error: Couldn't build bowtie index with err = 1"
... You could do it two ways. Either just align to cDNA without using GTF. Or use the whole genome/GTF with a special initial TopHat run which makes the transcriptome specific sequence index. Read about the second method on [TopHat manual page][1] (using TopHat section `--transcriptome-index ` part). ...
written 4 hours ago by genomax37k
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Comment: C: Samtools view command, Exec format error while trying to view a human chromosome
... You need to first sort original bam. Let that complete (no `.tmp` files should remain). Then index the sorted file. Finally do: `samtools view filename.sorted.bam chr6:xx-xx` That is the correct order. ...
written 7 hours ago by genomax37k
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Comment: C: Samtools view command, Exec format error while trying to view a human chromosome
... That name is just a place holder. If you were able to successfully sort your bam file then use whatever file name you have for that sorted file. Since you have the `.tmp` files still around you were NOT able to successfully complete the sorting of the bam file. So you would need to repeat that. Th ...
written 7 hours ago by genomax37k
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Comment: C: Samtools view command, Exec format error while trying to view a human chromosome
... Which version of `samtools` are you using? Have you tried `samtools view filename.sorted.bam chr6:xx-xx`? You do not use the `.bai` file. You just need to have it available in the same directory. ...
written 8 hours ago by genomax37k
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Comment: C: BBMap output meaning
... Tagging: https://www.biostars.org/u/14684/ ...
written 8 hours ago by genomax37k
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Comment: C: BBMap output meaning
... #InsertSize Count First column should be insert size and second column is count of fragments with that insert size. Have you scanned/trimmed this data? Can you try that? I will tag @Brian Bushnell on this thread so he can offer his take. Please be aware that he has been busy of late and ...
written 8 hours ago by genomax37k
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Comment: C: Questions about Reference Sequence in DESeq2
... Contact Geneious tech support since you have a license for the software. They can tell you where the annotations came from. ...
written 8 hours ago by genomax37k
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Comment: C: BBMap output meaning
... I am not sure why you have insert sizes that small and with quite a few counts as well. Has this data been trimmed? You probably should have set a `minlen=25` when you trimmed the data to avoid getting very short reads. ...
written 8 hours ago by genomax37k
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Comment: C: Getting Error with bowtie2! "Error: Couldn't build bowtie index with err = 1"
... Please do not use TopHat for new projects unless you have an absolute need to. Use STAR, BBMap, HISAT2 which are newer recommended programs. If you are going to use an annotation file then you should not use just the cDNA sequence. You should get the sequence of the full genome. Coordinates in yo ...
written 8 hours ago by genomax37k
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Comment: C: Remove vector sequences
... Have you tried BLAT? Does the BAC sequence otherwise look reasonable i.e. it maps to the right genome etc. ...
written 8 hours ago by genomax37k

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Commentator 1 day ago, created a comment with at least 3 up-votes. For C: Google genomics cloud platform ?
Commentator 2 days ago, created a comment with at least 3 up-votes. For C: Google genomics cloud platform ?
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: over presented kmer in fastq
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: over presented kmer in fastq
Scholar 5 days ago, created an answer that has been accepted. For A: Redirecting the Log.txt file from a STAR indexing run
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Scholar 9 days ago, created an answer that has been accepted. For A: Redirecting the Log.txt file from a STAR indexing run
Commentator 9 days ago, created a comment with at least 3 up-votes. For C: Google genomics cloud platform ?
Scholar 9 days ago, created an answer that has been accepted. For A: Redirecting the Log.txt file from a STAR indexing run
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: over presented kmer in fastq
Scholar 11 days ago, created an answer that has been accepted. For A: Redirecting the Log.txt file from a STAR indexing run
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Commentator 15 days ago, created a comment with at least 3 up-votes. For C: Is there a way to download FASTq files from SRR IDs?
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Good Answer 24 days ago, created an answer that was upvoted at least 5 times. For A: Professor assign me some tasks, gene ontology sucks. Anyone please guide me, i a

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