Activity for Lep-Anchor
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Tami Leanne Hildahl modified a comment on discussion General Discussion
Dear Pasi, We have generated a hybrid de novo assembly for a fish species (using long and short reads) and are looking at the best way to combine linkage mapping and Hi-C proximity to improve anchoring in draft chromosomes. A Hi-C anchored genome has already been developed from the de novo assembly, and linkage mapping data from an F1 cross has become available. Would you recommend using the linkage map data in Lep-Anchor with the Hi-C scaffolds to correct misalignments, or would it be wiser to scaffold...
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Dear Pasi, We have generated a hybrid de novo assembly for a fish species (using long and short reads) and are looking at the best way to combine linkage mapping and Hi-C proximity to improve anchoring in draft chromosomes. A Hi-C anchored genome has already been developed from the de novo assembly, and linkage mapping data from an F1 cross has become available. Would you recommend using the linkage map data in Lep-Anchor with the Hi-C scaffolds to correct misalignments, or would it be wiser to scaffold...
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Lep-Anchor updated /binary+code.zip
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Rastas Pasi M A committed [78dfa4] on Code
automatic noChromosome
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Pasi Rastas committed [607af1] on Code
liftover score fix, Map2Bed, etc.
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Rastas Pasi M A committed [ada270] on Code
chr=>chromosome in FitStepFunction
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Rastas Pasi M A committed [5993d7] on Code
FitStepFunction usage and snps
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Rastas Pasi M A committed [00103b] on Code
FitStepFunction usage and snps
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ChainPaf, etc.
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Thanks Hongbo, for pointing the missing file. The file is now added. Cheers, Pasi
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Rastas Pasi M A committed [e01d9f] on Code
cuts2paf
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Hongbo WANG modified a comment on discussion General Discussion
Dear Pasi, Thank you for developing this outstanding tool! Regarding the reference wiki instruction: #create a paf to fix possible false positives awk -f cuts2paf.awk errors.txt errors.txt >errors.paf I'm unable to locate the 'cuts2paf.awk' file. Could you provide guidance on this? Additionally, for processing 10x BAM files, should we use 'pro10x.awk', similar to how HiC data is processed? For example: hic bwa mem -t32 -5SPM reference.fasta.gz read1.fq.gz read2.fq.gz | samblaster -r | awk -f hic.awk...
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Dear Pasi, Thank you for developing this outstanding tool! Regarding the reference wiki instruction: create a paf to fix possible false positives awk -f cuts2paf.awk errors.txt errors.txt >errors.paf I'm unable to locate the 'cuts2paf.awk' file. Could you provide guidance on this? Additionally, for processing 10x BAM files, should we use 'pro10x.awk', similar to how HiC data is processed? For example: hic bwa mem -t32 -5SPM reference.fasta.gz read1.fq.gz read2.fq.gz | samblaster -r | awk -f hic.awk...
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java locale fix
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wrappers with markerSupport, ChainPaf
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FitStepFunction
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GammaModel
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Rastas Pasi M A committed [541149] on Code
CI fix
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Rastas Pasi M A committed [1bf45d] on Code
CI fix
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Rastas Pasi M A committed [71a790] on Code
ChainPaf
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small fixes
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ChainPaf fix and speedup
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ChainPaf fix
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paf2chain.awk
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ChainPaf etc.
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Rastas Pasi M A committed [232671] on Code
FitStepFunction bug fix
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Rastas Pasi M A committed [96c0ba] on Code
--contigMode in wrappers
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Rastas Pasi M A committed [4bc8a9] on Code
ld.awk
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Rastas Pasi M A committed [73143d] on Code
new wrappers
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Rastas Pasi M A committed [366eba] on Code
ChainPaf
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Dear Tami, I am looking at the Marey again... I can come up with two solutions: 1) just remove the 207 SNPs. 2) There is a long non-recombining region in one sex (male?) in LG14. Sometimes such regions are improved by the set "scale=M/N 1" in OrderMarkers2. This way you won't get the so much noise at the map ends. Maybe the problem disappears then. Cheers, Pasi
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Dear Pasi, If I trim the first group (n=127 SNPs) from my ordered trim plot out, I still have a bit of a funny marey. In trimming both the first and second groups (n=207 SNPs), then it is much improved. This is a much larger trim than any of my other groups (see attached files). Is that acceptable? I am attempting to run it through without JoinSingles to see if that improves the outcome as JS added >100 markers to that LG. Thoughts appreciated. Thank you, Tami
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Dear Pasi, I see. All of my groups received an initial 100 rounds of ordering, after which best likelihood was chosen, followed by trimming and another 50 rounds of ordering to determine best likelihood prior to continuing the pipeline. I will try trimming and re-ordering. Thank you, Tami
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Dear Tami, There is something strange in the group 14 map, but I cannot be sure what. I would run OrderMarkers2 one or two times on this group and see if the likelihood improves and the result looks better. As the Marey does not show similar pattern (as far as I can see), it is possible that trimming the strange pattern from the map start would be ok. Cheers, Pasi
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Dear Pasi, Correct. The larger file has all of my Mareys. I believe I did the LMPlot correctly, please see attached. Thanks, Tami
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Dear Tami, Could you please calculate the LMPlot for group 14? I can comment on it as this might be difficult concept. And yes, the latter is not Marey but is the Marey in former? Cheers, Pasi
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The ordered.14.trim file isn't a marey map, if that is what you're asking. It is simply ordered so I can look at it before trimming during LepMap.
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Dear Tami, Is the group 14 the same in both Mareys? They look very different. In ordered.14.trim.pdf markers 130-200 seem strange, like an inversion in map. You can construct the LMPlot graph to see if these markers are inverted in the map. If they are, running OrderMarker2 again on this chr should fix the problem. Cheers, Pasi
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Dear Pasi, I'm sorry, I missed your response earlier. I managed to fix this issue myself. However, I have a new query. I have worked out my marey maps so that they are much improved; although one linkage group (14) looks odd to me and I would appreciate it if you would give it a look. I have attached all of my trimmed maps and the ordered trim file for LG14 from lepmap. Thoughts appreciated. Tami
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Rastas Pasi M A committed [319e46] on Code
ChainPaf.java
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FitStepFunction keeps phase
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Dear Tami, Great that there is improvement; It is very crucial that the pedigree is correct before linkage mapping. And Lep-MAP3 can work nicely with a single parent, you can just add dummy mother. I think this has very small effect on filtering etc. so no need to worry. 300cM seems quite high, and for some species most maps are 50cM. I don't think the paf is affecting that. Lep-MAP3 has the tendency to put some false/erroneous markers at the map ends. You can probably just remove them to shorten...
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Dear Pasi, My marey maps are much improved after removing the false mother. However, they are ~300cM long. My trim plots from Lep-Map3 have my linkage groups ~50cM, which is correct. I am providing a PAF file during Lep-Anchor; is that, perhaps, causing the expansion of the linkage group? Please advise. Tami
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Dear Pasi, I did go back to confirm the pedigree and it appears the assigned mother is not related to our offspring. Is this as simple as updating the pedigree with a dummy variable for the mother? Or perhaps it would be wiser to re-filter the raw total SNPs after removing her? Thoughts appreciated. Thank you, Tami
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I should also note that the average recombination rate was 18.5.
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I should also note that the average recomination rate was 18.5.
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Dear Pasi, These are the position intervals. I agree, the backbone looks decent for most. Yes, the pedigree is correct; it is a single family cross. With regard to the contig length of the unused ones, I would have to check. "Short ones" by comparison? The Quast report indicated nearly all were >10,000bp, 1550/2039 were >/=25,000 and 1275/2039 were >/= 50,000bp. I did run haplotyper prior to attempting LepMap3. Cheers, Tami
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Dear Pasi, These are the position intervals. I agree, the backbone looks decent for most. Yes, the pedigree is correct; it is a single family cross. With regard to the contig length of the unused ones, I would have to check. "Short ones" by comparison? The Quast report indicated nearly all were >10,000bp, 1550/2039 were >/=25,000 and 1275/2039 were >/= 50,000bp. Cheers, Tami
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Dear Tami, The Mareys are indeed a bit scattered. Are these the raw map positions or position intervals? Anyway you can see the "backbone" of the Marey and it seems ok. Are you sure your pedigree is correct? And are the shortest contigs unused? Typically the shortest contigs do not have markers and they might leave out. Short ones might also be haplotypes. Cheers, Pasi
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Dear Pasi, Happy New Year! I would appreciate your input on my marey maps as they are quite messy. I ran through the LepMap3 pipeline prior to using LepAnchor to which I am also providing the mapped long reads. Additionally, it appears as if 1346 of my contigs (out of 2039) were unused, which does not seem correct. Should I return to LepMap3 and re-run something specific or is there something I can do in LepAnchor? Advice appreciated. Tami
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