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Search: Posts Made By: sfh838t
Forum: Bioinformatics 12-07-2018, 04:47 AM
Replies: 3
Views: 952
Posted By sfh838t
Thank you GenoMax. the header suggestion almost...

Thank you GenoMax.
the header suggestion almost worked, in one case, not so much in the other because it is too long I suspect.
and thanks for the BBsplit suggestion as well.It obviously does...
Forum: Bioinformatics 12-05-2018, 10:30 AM
Replies: 3
Views: 952
Posted By sfh838t
SAM header, difference between using sam tools or awk to filter ?

I have filtered SAM files to get only the aligned reads with samtools view -F4.
my output is a file in SAM format, the header is lost, but I can still convert the file to BAM and then use...
Forum: Bioinformatics 02-28-2018, 06:11 AM
Replies: 5
Views: 2,202
Posted By sfh838t
Thanks again. I had not found the manual yet.

Thanks again. I had not found the manual yet.
Forum: Bioinformatics 02-28-2018, 04:58 AM
Replies: 5
Views: 2,202
Posted By sfh838t
BBmap not finishing

Removing the white space after the equal sign has started BBmap running, but it has been running now (or seems to be at least, there is activity in system monitor) for about 20 hours.
I had one...
Forum: Bioinformatics 02-27-2018, 09:35 AM
Replies: 5
Views: 2,202
Posted By sfh838t
Jeez, would have never suspected that! Don't...

Jeez, would have never suspected that! Don't know if it will run through to the end ok, but it is running! thanks you very much!
Forum: Bioinformatics 02-27-2018, 07:15 AM
Replies: 5
Views: 2,202
Posted By sfh838t
problems with BBmap/java

hi,
I am trying to use BBmap to dedupe illumina paired end reads. (tried fastuniq but can't get past the "error in open left file first_read_name" error)
command line I used:
dedupe.sh in1=...
Forum: General 02-09-2017, 08:19 AM
Replies: 8
Views: 1,640
Posted By sfh838t
Ok, I did install and use this clumpify tool. ...

Ok, I did install and use this clumpify tool.
and it did not make any difference. it found some 300 duplicates, I assemble slightly fewer reads, to similar n50 and total nt count and of the contigs...
Forum: General 02-09-2017, 06:35 AM
Replies: 8
Views: 1,640
Posted By sfh838t
I did see Brians post, but did not check on that...

I did see Brians post, but did not check on that so far. Looks like I will have to take the plunge and install yet another toolbox. Let's see what will go wrong this time.....:)
Forum: General 02-09-2017, 05:10 AM
Replies: 8
Views: 1,640
Posted By sfh838t
these are single end reads from an RNA sequencing...

these are single end reads from an RNA sequencing project. adapter sequences have been removed.
out of some 37 mil reads I get 4000 reads reads aligning to a just under 8000bp long virus that we...
Forum: General 02-08-2017, 01:18 PM
Replies: 8
Views: 1,640
Posted By sfh838t
reads align but contigs do not??

Here is something that puzzles me:
I have 4000 reads that align to my reference genome. I can visualize them, they cover maybe 80 % or a little more of the reference sequence.
I assemble these...
Forum: RNA Sequencing 09-01-2016, 10:21 AM
Replies: 0
Views: 963
Posted By sfh838t
viral small RNA that is NOT siRNA

Hi all, while looking for SNPs for virus quasispecies in a badnavirus using RNA that was gel-excised with maximum length of 100, maybe 200 bp I find definitive read alignment hotspots to the master...
Forum: RNA Sequencing 03-16-2016, 07:16 AM
Replies: 10
Views: 3,029
Posted By sfh838t
it was the second question, so I don't know if it...

it was the second question, so I don't know if it should be split.
I will look into tadpole and the other suggestions, thanks!
Forum: RNA Sequencing 03-16-2016, 06:17 AM
Replies: 10
Views: 3,029
Posted By sfh838t
looking for variants, maybe strain identification...

looking for variants, maybe strain identification etc.
velvet seems to be commonly used for this, any suggestions for a different assembler?
Forum: RNA Sequencing 03-16-2016, 06:12 AM
Replies: 10
Views: 3,029
Posted By sfh838t
yes, you did understand correctly. I used...

yes, you did understand correctly.
I used either BWA or bowtie2 to align reads to ref seq, then go through the samtools steps to filter out only reads that align, convert back to fastq, then run...
Forum: RNA Sequencing 03-16-2016, 05:53 AM
Replies: 10
Views: 3,029
Posted By sfh838t
I used cutadapt for adapter removal which best...

I used cutadapt for adapter removal which best that I can tell will remove all parts of the search string no matter where they occur.
It still puzzles me though why I can find reads that align...
Forum: RNA Sequencing 03-15-2016, 12:50 PM
Replies: 10
Views: 3,029
Posted By sfh838t
thank you. I can see the nonsense part . and yes,...

thank you. I can see the nonsense part . and yes, it was 36nt after adapter removal.
Forum: RNA Sequencing 03-15-2016, 10:50 AM
Replies: 10
Views: 3,029
Posted By sfh838t
why are sRNA output reads longer than siRNA?

Hi,
this is possibly a dumb question, but if my goal is to find siRNA (20-25 nt long) why are the Illumina reads 36 nt long, at least before quality trim? if a 24 nt long RNA piece (plus...
Forum: De novo discovery 03-01-2016, 10:32 AM
Replies: 1
Views: 3,532
Posted By sfh838t
localized consensus build instead of scaffolding

I am trying to make something out of a denovo, heterozygous plant WGS.
it won't go past a contig stage (scaffolding improved average contig length by 1 nt!) for several reasons.
However, the ref...
Forum: General 03-02-2015, 11:54 AM
Replies: 10
Views: 2,420
Posted By sfh838t
Thanks, I will try that.

Thanks, I will try that.
Forum: General 02-24-2015, 11:43 AM
Replies: 10
Views: 2,420
Posted By sfh838t
I did get the GATK answer and now have a file...

I did get the GATK answer and now have a file with both together. working with plants and all bets are off :) the samtools output might remain a mystery .
Probably a new question: does anyone know...
Forum: General 02-24-2015, 10:18 AM
Replies: 10
Views: 2,420
Posted By sfh838t
ok, I just went and looked at reads and see the...

ok, I just went and looked at reads and see the same insert that I identified in contigs. this is important for the project, because this insert is present in one possible parent but not the other.
Forum: General 02-24-2015, 10:07 AM
Replies: 10
Views: 2,420
Posted By sfh838t
I look at contigs in IGV and see both SNPs and...

I look at contigs in IGV and see both SNPs and indels. Have not looked at reads.
Forum: General 02-24-2015, 10:03 AM
Replies: 10
Views: 2,420
Posted By sfh838t
yes, I can see both indels and SNPs in IGV. most...

yes, I can see both indels and SNPs in IGV. most of them are 3-7 bp long. And the indels found are at different locations than the SNPs found.
Is it legitimate to use contigs in calling variants?
Forum: General 02-24-2015, 09:53 AM
Replies: 10
Views: 2,420
Posted By sfh838t
All my alignments are done using BWA, and the...

All my alignments are done using BWA, and the same file of reads was used for both GATK and samtools.
I used the samtools mpileup/bcftools/vcfutils steps both times:
samtools +reads = only SNPs...
Forum: General 02-24-2015, 08:37 AM
Replies: 10
Views: 2,420
Posted By sfh838t
variant calling in plant

I am trying to get all variants of all types for a sequence I put together through an assembly step followed by consensus building using a reference. Now I am looking for variants. I have used...
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